Thursday, October 9, 2008

Pharma companies in india

Click the following URL and you can get the list of the pharmacutical companies:

http://www.naukri2000.com/careers/pharmaceutical.php3
BIOINFORMATICS AND BIO TECH COMPANIES

BIOINFORMATICS COMPANIES:
· www-3.ibm.com
· www.3rdmill.com
· www.4-sci.com
· www.GenomicTechnologies.com
· www.PharmaDM.com
· www.abergc.com
· www.aborygen.com
· www.accelrys.com
· www.acdlabs.com
· www.acero.com
· www.aclara.com
· www.advancedcell.com
· www.affymetrix.com
· www.agencourt.com
· www.agilebio.com
· www.agrogene.com
· www.algan.com
· www.algonomics.com
· www.allometra.com
· www.almabioinfo.com
· www.alphadna.com
· www.amartus.com
· www.amaxa.com
· www.amebioscience.com
· www.amita.com
· www.ananomouse.com
· www.anedabio.com
· www.antivirals.com
· www.apocom.com
· www.applied-maths.com
· www.appliedbiosystems.com
· www.aptagen.com
· www.ariadnegenomics.com
· www.arraygenetics.com
· www.artificial-life.com
· www.atglabsinc.com
· www.autohandle.com
· www.axontologic.com
· www.base4.com
· www.benitec.com.au
· www.bforrester.com
· www.bio-link.org
· www.bioalma.com
· www.bioanalyticsgroup.com
· www.biobase.de
· www.biocarta.com
· www.biochipnet.com
· www.bioclon.com
· www.biodata.ee
· www.biodatabases.com
· www.biodiscovery.com
· www.bioforensics.com
· www.biognostik.com
· www.bioinformaticist.biz
· www.bioinformatics.co.uk
· www.bioinformatics.csiro.au
· www.bioinformaticsservices.com
· www.bioinformaticssolutions.com
· www.bioinformatik.de
· www.bioit-il.com
· www.biolateral.com.au
· www.biomax.com
· www.biomax.de
· www.biomedcomp.com
· www.biomind.com
· www.bioplanet.com
· www.biosentients.com
· www.biosiris.com
· www.biosis.org
· www.biosoft.com
· www.biosoftsolutions.de
· www.biosolve.de
· www.biospec.com
· www.biotiquesystems.com
· www.biotools.com
· www.biowell.com.tw
· www.biowisdom.com
· www.bioxtal.com
· www.bluespeed.net
· www.bmi-heidelberg.com
· www.caesar.de
· www.caesarsoftware.com
· www.cambridgeantibody.com
· www.cambridgebluegnome.com
· www.cbssci.com
· www.celera.com
· www.cellectis.com
· www.centagenetix.com
· www.ceuticalsoft.com
· www.cgen.com
· www.changbioscience.com
· www.chemcomp.com
· www.chemgenes.com
· www.cimsoft.com
· www.clcbio.com
· www.clearlinetech.com
· www.clonaid.com
· www.clondiag.com
· www.cmrsinc.com
· www.cognia.com
· www.colnow.com
· www.compass.com.ph
· www.compassgenomics.com
· www.compudrug.com
· www.compugen.co.il
· www.concurrentpharma.com
· www.corelims.com
· www.corimbia.com
· www.correlogic.com
· www.cresset-bmd.com
· www.crti.com
· www.cybergene.se
· www.cybgen.com
· www.d-trends.com
· www.davissequencing.com
· www.decode.com
· www.decodon.com
· www.definiens.com
· www.deltagen.com
· www.deosystems.com
· www.designergenesinc.com
· www.discoverypartners.com
· www.dna-software.com
· www.dna.com
· www.dnastar.com
· www.dnatools.com
· www.doubletwist.com
· www.duii.com
· www.dxsgenotyping.com
· www.dynacom.co.jp
· www.e-proteomics.net
· www.egenetics.com
· www.eidogen.com
· www.elitra.com
· www.elixirpharm.com
· www.employstrat.com
· www.entelos.com
· www.epigenomics.com
· www.epistasis.org
· www.epitope-informatics.com
· www.eragen.com
· www.esearchinternational.net
· www.essentialinformatics.com
· www.etexxbio.com
· www.evprecruit.com
· www.expasy.ch
· www.eyesopen.com
· www.familytreedna.com
· www.fqspl.com.pl
· www.fractalgenomics.com
· www.functional-genetics.com
· www.gemini-genomics.com
· www.genStruct.com
· www.genaissance.com
· www.genamics.com
· www.gene-alliance.com
· www.gene-biotech.com
· www.gene-chips.com
· www.gene-it.com
· www.gene-quantification.de
· www.gene2drug.com
· www.geneart.com
· www.genebio.com
· www.geneco.com
· www.genecodes.com
· www.genedata.com
· www.geneformatics.com
· www.genego.com
· www.genelink.com
· www.genelogic.com
· www.genemachines.com
· www.genepilot.com
· www.genesearch.com.au
· www.genesifter.net
· www.genestudio.com
· www.genesynthesis.org
· www.genetargeting.com
· www.genetherapysystems.com
· www.genetic-id-services.com
· www.geneticXchange.com
· www.geneticxchange.com
· www.genetix.com
· www.genfit.com
· www.genmatrix.com
· www.genodyssee.com
· www.genologics.com
· www.genolyze.com
· www.genomatica.com
· www.genomatix.com
· www.genomatix.de
· www.genometrician.com
· www.genomica.com
· www.genomicdiscoverytools.com
· www.genomicsinc.com
· www.genomicsolutions.com
· www.genomictechnologies.com
· www.genomining.com
· www.genomix.com
· www.genops.com
· www.genoptix.com
· www.genset.fr
· www.gentech.fr
· www.geospiza.com
· www.glycominds.com
· www.gnsbiotech.com
· www.goldenhelix.com
· www.gtc-bio.com
· www.helixinfosystems.com
· www.hessjobs.com
· www.hippron.com
· www.hybridon.com www.ibiomatics.com
· www.idrtech.com
· www.idtdna.com
· www.illumina.com
· www.imagingresearch.com
· www.imaxia.com
· www.imphasis.com
· www.incellico.com
· www.incogen.com
· www.incyte.com
· www.informagen.com
· www.informaxinc.com
· www.inforsense.com
· www.ingenovis.com
· www.ingenuity.com
· www.innaphase.com
· www.innomedical.com
· www.inpharmatica.co.uk
· www.inpharmatica.com
· www.inpharmix.com
· www.insightful.com
· www.insilico-biotechnology.com
· www.insilico.com
· www.insilicolabs.com
· www.insilicos.com
· www.interactiva.de
· www.intronn.com
· www.inveniobio.com
· www.invitrogen.com
· www.io-informatics.com
· www.iobion.com
· www.iper1.com
· www.it-omics.com
· www.iuvita.com
· www.jaexecutivesearch.com
· www.jubilantbiosys.com
· www.katonahgroup.com
· www.kennatechnologies.com
· www.kerberholtdevol.com
· www.kinematik.com
· www.knowledge.com
· www.koada.com
· www.kooprime.com
· www.labbook.com
· www.labdb.com
· www.lablogic.com
· www.labonweb.com
· www.labvantage.com
· www.lambdaplus.com
· www.lazaron.com
· www.lifesciencesworld.com
· www.lionbioscience.com
· www.lloydstaffing.com
· www.lsbio.com
· www.ludesi.com
· www.lynxgen.com
· www.macrogen.com
· www.mag.com
· www.mantik.de
· www.markergene.com
· www.mastl.com
· www.mathecology.com
· www.matrixscience.com
· www.mdli.com
· www.medbioworld.com
· www.medicel.com
· www.medigenomix.de
· www.mendelbio.com
· www.meta-helix.com
· www.metabolic-explorer.com
· www.metalife.de
· www.metaphorics.com
· www.microdiscovery.de
· www.microrite.com
· www.midilabs.com
· www.miraibio.com
· www.mirusbio.com
· www.mol-net.de
· www.molecularconnections.com
· www.molecularmed.com
· www.molecularmining.com
· www.molecularware.com
· www.molmine.com
· www.molsoft.com
· www.mpi-softtech.com
· www.mri-boston.com
· www.mutransposon.org
· www.mutransposon.orgwww.worksinc.com
· www.myriad.com
· www.nadii.com
· www.neomorphic.com
· www.netgenics.com
· www.netid.com
· www.newportsearch.com
· www.nonlinear.com
· www.nuvelo.com
· www.ocimumbio.com
· www.od260.com
· www.ogs.com
· www.oligos.com
· www.omnigon.com
· www.omniviz.com
· www.ontrackpro.com
· www.origenel.com
· www.ozgene.com
· www.packardbiochip.com
· www.pangenex.com
· www.paracel.com
· www.partek.com
· www.peoplesgenetics.com
· www.petagen.com
· www.ppl-therapeutics.com
· www.predictivepatterns.com
· www.premierbiosoft.com
· www.primegenbiotech.com
· www.proceryon.com
· www.proconverse.com
· www.progeny2000.com
· www.proglab.se
· www.prolume.com
· www.prosanos.com
· www.proteinmechanics.com
· www.proteom.com
· www.proteomeconsult.com
· www.proteomes.co.kr
· www.pubgene.com
· www.puretechventures.com
· www.q-pharm.com
· www.qgene.com
· www.quantiom.de
· www.rabbithutch.com
· www.receptorscience.com
· www.redasoft.com
· www.redstormscientific.com
· www.reeltwo.com
· www.relevantsoftware.com
· www.rescentris.com
· www.rii.com
· www.rosettabio.com
· www.sas.com
· www.savingsandclone.com
· www.science-factory.com
· www.scinovaindia.com
· www.scitechint.com
· www.scitegic.com
· www.sdc.co.jp
· www.searchfirm.com
· www.seascapelearning.com
· www.seattlegenetics.com
· www.semantxls.com
· www.seqbio.com
· www.sequenom.com
· www.sequiturinc.com
· www.seqwright.com
· www.sgi.com
· www.sgxpharma.com
· www.sigenetics.com
· www.silicoinsights.com
· www.silicongenetics.com
· www.simulations-plus.com
· www.softberry.com
· www.softgenetics.com
· www.soonersci.com
· www.spotfire.com
· www.spsoft.com
· www.spss.com
· www.sratemecula.com
· www.stafftopia.com
· www.starbridgesystems.com
· www.stewartgroup.net
· www.strandgenomics.com
· www.strubix.com
· www.sunflaremarketing.com
· www.synamatix.com
· www.syngene.com
· www.syngentabiotech.com
· www.teranode.com
BIO TECH COMPANIES:
· www.5prime.com
· www.actelion.com
· www.addgene.org
· www.affymetrix.com
· www.agricultureb2b.com
· www.amershambiosciences.com
· www.amgen.com
· www.antibodies-online.com
· www.ariad.com
· www.arpida.com
· www.astrazeneca.com
· www.atheris.ch
· www.aurorafinechemicals.com
· www.base-asia.com
· www.basilea.com
· www.bayer.com
· www.biacore.com
· www.bio-balance.com
· www.bio-rad.com
· www.biogen.com
· www.bioimage.com
· www.bioportfolio.com
· www.biospecifics.com
· www.biosystematica.com
· www.biovision.de
· www.caprion.com
· www.cbclickbank.com
· www.celera.com
· www.cellectis.com
· www.cellsignal.com
· www.celltech.com
· www.cellzome.com
· www.centocor.com
· www.chemsuppliers.org
· www.ciphergen.com
· www.clontech.com
· www.cognetix.com
· www.csl.com.au
· www.curagen.com
· www.cytos.com
· www.decode.com
· www.destiny-pharma.demon.co.uk
· www.directory.blauplanet.com
· www.diversa.com
· www.drugdevelopment-technology.com
· www.emeraldbiostructures.com
· www.encysive.com
· www.entelechon.com
· www.entelos.com
· www.envirologix.com
· www.enzon.com
· www.epidauros.com
· www.esbatech.com
· www.evotec.de
· www.exchemistry.com
· www.exelixis.com
· www.fermentas.com
· www.gbiosciences.com
· www.gelcompany.com
· www.genaissance.com
· www.gene.com
· www.genencor.com
· www.geneprot.com
· www.genetics.com
· www.genomex.com
· www.genomicsolutions.com
· www.genwaybio.com
· www.genzyme.com
· www.geron.com
· www.gsk.com
· www.helixbiopharma.com
· www.hgsi.com
· www.hoechst.com
· www.hri.co.jp
· www.hybrigenics.com
· www.hyseq.com
· www.hytest.fi
· www.illumina.com
· www.incyte.com
· www.integratedgenomics.com
· www.invitrogen.com
· www.jovasolutions.com
· www.kudospharma.co.uk
· www.larova.com
· www.lilly.com
· www.lsbc.com
· www.lynxgen.com
· www.memorec.com
· www.migenix.com
· www.millipore.com
· www.mitsuichemicals.com
· www.mlnm.com
· www.mologen.com
· www.myriad.com
· www.neb.com
· www.ngi.com
· www.nonlinear.com
· www.novartis.com
· www.novo.dk
· www.ocimumbio.com
· www.organic-chemistry.org
· www.pfizer.com
· www.pharmacopeia.com
· www.pharmingen.com
· www.pharsight.com
· www.phrma.org
· www.poseidonprobes.com
· www.prionics.com
· www.promega.com
· www.proteome.com
· www.proteomesystems.com
· www.prozyme.com

Thursday, September 25, 2008

4PEAKS

Overview
4Peaks is a program that helps molecular biologists to visualize and edit their DNA sequence files. At last there is a decent solution for analyzing trace files on the MacOSX platform, taking another step away from slow and non-native programs from the MacOS9 period. Also, 4Peaks supports most commonly used sequence file formats right out of the box, you no longer have to convert them first using AppleScripts or other painstaking methods. Analyzing your sequence was never so much fun! Download >>

Key Features

Move mouse over buttons to learn more...
For Peaks - 4Peaks can read and write most common trace file formats, and allows direct access to both sequence and translation. It offers the ability to analyze, edit and correct your sequence data. 4Peaks leverages MacOSX strong foundation to bring you the best sequence trace viewer available. period.
New Features in 4Peaks 1.7

The latest version of 4Peaks is now fully compliant with MacOSX 10.4 Tiger. In addition, it now runs natively on Intel-based Macs. Finally, we continued fixing a number of reported bugs.

Wednesday, September 24, 2008

Gene structure Prediction tool

TIGR-Glimmer: Glimmer are for identification of possible genes for prokaryotes sequences . It is based on interpolated Markov models to identify the coding regions and distinguish them from noncoding DNA.Download Glimmer Via FTP
TIGR-GlimmerM: A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programing algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. Download Glimmer Via FTP
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Alignment and Similarity searching tools

EBI- Fasta executable: Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs. Fasta can be very specific when identifying long regions of low similarity especially for highly diverged sequences.Download EBI-Fasta executable via FTP
EBI-Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.Download EBI-Clustal W via FTP
Clustal X: Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. Download Clustax (Windows OS)
TIGR-MUMmer(fast alignment of large-scale DNA and protein sequences):A system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides. Download MUMer Via FTP
TIGR-AAT package(A tool for analyzing and annotating genomic sequences): The AAT package includes two sets of programs, one set (DPS/NAP) for comparing the query sequence with a protein database, and the other (DDS/GAP2) for comparing the query with a cDNA database (Huang et al., 1997).Download AAT package via FTP

Monday, September 22, 2008

Binding Affinity Prediction of Protein-Ligand Server(BAPPL)

BAPPL server
HIV-I Protease complexed with U75875 (1hiv.pdb)
Welcome to the BAPPL server
Binding Affinity Prediction of Protein-Ligand (BAPPL) server computes the binding free energy of a non-metallo protein-ligand complex using an all atom energy based empirical scoring function
[1] & [2].
BAPPL server provides two methods as options:
Method 1 : Input should be an energy minimized protein-ligand complex with hydrogens added, protonation states, partial atomic charges and van der Waals parameters (R* and ε) assigned for each atom. The server directly computes the binding affinity of the complex using the assigned parameters. For format specifications on the input, please refer to the README file.Method 2 : Input should be an energy minimized protein-ligand complex with hydrogens added and protonation states assigned. The net charge on the ligand should be specified. The server derives the partial atomic charges of the ligand using the AM1-BCC procedure [3] and GAFF [5] force field for van der Waals parameters. Cornell et al. force field [4] is used to assign partial atomic charges and van der Waals parameters for the proteins. For format specifications on the input, please refer to the README file.
For the purpose of validation of the empirical scoring function
[1] a dataset of 161 non-metallo protein-ligand complexes has been prepared. Click here to access the Protein-Ligand Complex Dataset.
BAPPL server
-->
E-Mail
E-mail address



E-Mail
E-mail address


-->
Select Option
Method 1 Method 2 Net Ligand Charge 0 -10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 +1 +2 +3 +4 +5 +6 +7 +8 +9 +10
Input PDB file E-mail address
Upload
Input PDB file







-->
Instructions for using the server
The input protein-ligand complex should follow the format described in the README files. In case of any differences, either an error is generated resulting in the termination of computation or the predicted binding affinity value will have errors in it.
Please specify the E-mail address, Name and Institution.
Choose either one of the options : "Method 1" OR "Method 2"
For Method 2, specify the Net ligand charge.
Browse and select the input file.(The input file name should not contain whitespace(s) & PDBID should be a four letter code, like 1a30.pdb)
Click Submit to get the result.
The Predicted Binding Affinity value will be sent via E-mail at the address specified. The computation may take 5-10 minutes depending upon the load on the web server and the number of atoms in the input file.
IMPORTANT: The predicted binding affinities are dependent upon:
The protonation states assigned to the ligand and protein atoms.
The procedure used to derive the partial atomic charges for ligand atoms like (AM1-BCC, HF/6-31G*/RESP, etc.) and the force field used to assign the partial atomic charges for the protein atoms like (AMBER, CHARMM, OPLS, etc.).
The force field used to assign the van der Waals parameters for ligand and protein atoms.
Energy minimization / geometry optimization protocol used to remove any clashes from the complex.
NOTE : The empirical scoring function
[1] has been calibrated using the HF/6-31G*/RESP equivalent partial atomic charges and Cornell et al. [4] and GAFF [5] force field parameters for proteins and ligands respectively. We have provided the AM1-BCC procedure for deriving partial atomic charges of ligands for Method 2 because this procedure is fast and produces charges of comparable accuracy to the HF/6-31G*/RESP method.
REFERENCES
[1] Jain, T. and Jayaram, B. (2005) An all atom energy based computational protocol for predicting binding affinities of protein-ligand complexes. FEBS Letters, 579, 6659-6666. [Abstract]
[2] Arora, N. and Jayaram, B. (1998) Energetic of base pairs in B-DNA in solution: An appraisal of potential functions and dielectric treatments. J. Phys. Chem. B. 102, 6139-6144. [Abstract]
[3] Jakalian, A., Bush, B.L., Jack, D.B. and Bayaly, C.I. (2000) Fast, efficient generation of high-quality atomic charges. J. Comput. Chem. 21, 132-146.
[4] Cornell, W.D. et al. (1995) A second generation force field for the simulation of proteins, nucleic acids and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
[5] Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A. and Case, D.A. (2004) Development and testing of a general amber force field. J. Comput. Chem. 25, 1157-1174.

Monday, September 15, 2008

SOFTGENETICS

SOFTGENETICS:

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Mutation Surveyor

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GeneMarker
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GeneMarker® for Multiplex Ligation-dependent Probe Amplification (MLPA*)
GeneMarker now has the capability to analyze data from Multiplex Ligation-dependent Probe Amplification (MLPA). Click here for more information on MLPA tests and test kits.
Current applications include the detection of exon deletions in the human BRCA1, MSH2 and MLH1 genes associated with breast cancer and colon cancer, detection of trisomies as in Down Syndrome (47, XX + 21), categorization of chromosomal abnormalities in cell lines and tumor samples, and mutation detection.
With GeneMarker, MLPA data analysis is an efficient, quick, and easy process, with features such as customized reporting, intensity comparison, data normalization, and printing.
GeneMarker is an excellent tool for nearly all Genotyping applications. The exclusive, high resolution gel image provides a quick overview of the MLPA analysis, allowing rapid discernment of areas of interest. The MLPA analysis accurately identifies exon deletions and duplications through calculating the intensity ratios of sample to control.
MLPA Normalization
GeneMarker can normalize MLPA derived data by an internal control probe method or an inter-lane population method. The user is able to specify the normalization method in the Run Wizard prior to analysis. The normalization is similar to that designed by Graham R. Taylor at St. James’s University Hospital, Leeds. You may find a detailed description of the method titled “Regression-enhanced examination of MLPA (REX-MLPA): towards automated and objective scoring” at http://leedsdna.info/science/dosage/REX-MLPA/REX-MLPA_CMGS04.ppt.
The internal control probe method normalizes the data by comparing the individual peak intensities within one sample lane. The inter-lane population method compares the peak intensities of the amplified probes between sample lanes. Both normalization methods take the square root of the intensity ratio and plot the ratios to model a linear regression, using the control probes as reference points.
MLPA Report
MLPA Intensity Report
GeneMarker is designed to identify copy number changes in genomic sequences. The main interface window after running the data is shown above. The various peaks in the electopherogram represent different amplified probes within the sample and can be labeled accordingly in the Panel Editor. The report displays the presence and absence of the amplified probes within each sample. The green flag is used to represent high quality peaks, whereas a yellow symbol is used to represent peaks with a lower score. This report may be saved as a text file for printing in Excel.
The user may also display the intensity for the peaks representing the amplified probes. Since MLPA is designed to locate exonic duplications and deletions, the peak intensity of the amplified probes is a very important factor in the analysis. The peak intensity is directly correlated to the copy number in the sample trace. This report may also be saved for printing in Excel.
MLPA Regression Plot
MLPA Intensity Ratio
The software forms a regression line utilizing a standard T distribution. The user may select an Increment or Decrement Regression to locate outliers within the data set. The software identifies outliers based upon a userdefined confidence limit. The report shown above displays the peak intensity ratio between sample and control sample for each amplified probe. The sample to control intensity ratio of probe HIRA in sample B5_11881 is 0.415. The user may also display the intensity of each probe, which in this case is 965 for the sample probe and 2323 for the control.
In order to identify copy number changes within the sample, the software uses the intensity ratios of sample to control. The user can define the thresholds dictating the exonic duplications and/or deletions. The report can display the peak intensity ratio, peak intensity, or peak area. Data points which lie outside the user defined threshold for deletion and duplication (indicated by the horizontal green lines) most likely have some significance for copy number change. The report can be saved as a text file and can be imported into Excel for printing.
*MLPA is a registered trademark of MRC-Holland.
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Copyright 2005. SoftGenetics, LLC. State College, PA USA 16803Phone: 814-237-9340 Fax: 814-237-9343 Email: info@softgenetics.com

DATA ANALYSIS SOFTWARE

Data Analysis Software from the BRC
The following software for genetic data analysis were developed and made available by researchers at or affiliated with the Bioinformatics Research Center:
Alternative Splicing Gallery (ASG) GDA QTL Cartographer Windows QTL Cartographer Forensic DNA Mixtures
Hy-Phy PowerMarker Mixed Models and QTLs Exact Tests Cytonuclear Disequilibria
Alternative Splicing Gallery (ASG) is a web-based splicing graph database that integrates transcript information from Ensembl, RefSeq, STACK, TIGR gene index, and UniGene, in order to explore and visualize gene structure and alternative splicing and to provide an exhaustive transcript catalog. The program was developed by Jeremy Leipzig and Dr. Steffen Heber.
Genetic Data Analysis (GDA) is a software package for analyzing discrete population genetic data. There are versions of GDA suitable for all Microsoft Windows platforms. The Lewis Lab Software Site has links for downloading the program over the web and instructions for downloading the program using anonymous FTP.
QTL Cartographer is a suite of programs to map quantitative traits using a map of molecular markers.
Windows QTL Cartographer maps quantitative trait loci in cross populations from inbred lines. It incorporates many of the modules found in its command-line sibling, QTL Cartographer (see above). WinQTLCart includes powerful graphic tools for presenting mapping results and can import and export data in a variety of formats.
DNAMIX v.3 calculates likelihood ratios for mixed DNA samples encountered in forensic science. It is platform-independent and is applicable to complex mixtures as well as single-contributor stains.
Hypothesis Testing Using Phylogenies (Hy-Phy) is a software package for maximum likelihood analyses of genetic sequence data. It is equipped with tools to test various statistical hypotheses.
PowerMarker, written by Jack Liu, is a comprehensive set of statistical methods for discrete genetic data analysis, designed especially for SNP/SSR data analysis. It also includes a 2-D Viewer and CoreSet batch system.
Mixed Models and QTLs: Programs for mixed model approaches for quantitative genetic analysis by Jun Zhu.
Exact conditional tests for different combinations of allelic and genotypic disequilibria on haploid and diploid data, or their combination. Get readme file, source code in UNIX archive, source code in MS-DOS archive, solaris2.6 executable, sgi-irix6.5 executable, MS Windows executable.
Cytonuclear Disequilibrium: Christopher J. Basten has written two programs for calculating cytonuclear disequilibria. These are MS Windows and Macintosh binaries as well as the UNIX distribution including source code and a makefile. All three distributions include example files and documentation. These programs have online manual pages.
For diallelic cytonuclear systems, see CNDd. For multiallelic systems, see CNDm.

Friday, August 22, 2008

RASMOL

Downloading RasMol
This page provides local copies of the RasMol program v2.6b2a. Although this is not the latest release, it has thus far been fine for use by our Biochemistry students.
The very latest release is 2.7.4.2. This is a collaborative effort and is still under development. Download the latest beta test version from http://openrasmol.org/
For instructions on how to use RasMol, take a look at the online RasMol Manual.
For more information about Rasmol and for links to other Rasmol resources, have a look at the Rasmol/Chime Home Page set up by Erik Martz at the University of Massachusetts.
Having problems?? Send me an email
Macintosh ComputersDownload the appropriate file.
RasMac2.6-68k.sit.hqx - RasMac version 2.6 Beta-2a for Apple Macintosh (68k)
RasMac2.6-PPC.sit.hqx - RasMac version 2.6 Beta-2a for Power Macintosh (PPC)
Note. These are compressed files. Many web browsers will automatically unstuff the files into a RasMac directory containing the appropriate RasMac application, some sample pdb files, and documentation (you will generally find the RasMac folder on the desktop). The documentation also includes a manual for the original RasMol v2.5 plus an abbreviated reference card. Note that the online RasMol Manual has been updated for version 2.6.
If the web browser does not unstuff the files automatically, save the file, then use StuffItExpander to decompress the file. The StuffItExpander utility is available from the Curtin Public Domain server under Macintosh:Utilities:Compression Utilities:StuffItExpander4.01(full). In this directory you will find the file 'StuffItExpander 4.01 Installer'. Double-click on the Installer file and follow the instructions for installation on your Macintosh hard drive. The StuffItExpander utility is also available on the web, try Aladdin Systems for the latest version.
Move the RasMac directory onto your hard drive. You should then configure your web browser to recognise RasMac as a helper application.
PC/WindowsDownload RASWIN.ZIP
This is a compressed file which unzips into a RasWin directory with the 32-bit RasWin v2.6 Beta-2a application (rw32b2a.exe) along with two help files (rasmol.hlp and raswin.hlp) needed by the application. The directory also includes a manual for the original RasMol v2.5 plus an abbreviated reference card. Note that the online RasMol Manual has been updated for version 2.6.
Use a decompression utility like PKUnzip to unzip the PC file if your web browser doesn't do so automatically. PKUnzip is available from the Curtin Public Domain Server under PC:UTILS:ARCHIVE:PKZ204G.EXE. Create a new directory (PKUNZIP) and download PKZ204G.EXE into this directory. Run PKZ204G.EXE under DOS. It will create the PKUnzip executables plus all documentation for the program. PKUnzip can also be downloaded from the web. Here is one site.
The 32-bit version of RasWin will run under Windows95 or WindowsNT as is.
Installation in Windows 95.
Right-click on Start and select Open. From the Start Menu window, double click to open the Programs window (or wherever you want RasMol to be). Now, use Windows Explorer to find the RasWin program file you downloaded (RW32B2A.EXE). Click the right mouse button on the RasWin program file, and select Create Shortcut. A new file will appear. Drag it into the Programs window (or wherever you want it). Close all windows. Now, the Start, Programs menu will have RasWin on its list. You should also configure your web browser to recognise RW32B2A.EXE as a helper application.
Installation in Windows 3.1x
Windows 3.1x can also run the 32-bit version, but you must have (i) an 80386 or better CPU, (ii) floating point hardware (this is built into 80486DX and Pentiums) and (iii) a free accessory provided by MicroSoft called Win32s installed with your Windows 3.1x. The latest upgrade is available as: Pw1118.exe via Web
Instructions for installation are found at the Microsoft site.
Once you have downloaded RasWin and installed Win32s, create a new program item for RasWin. In Windows, select File, New (Program Item), Browse, and select C:\RASWIN\RW32B2A.EXE, OK. In the Description field, put RasWin followed by the version you are installing (for example RasWin32 2.6 Beta2). In the Working Directory field, put C:\RASWIN or wherever you plan to keep your scripts and PDB (atomic coordinate) data files. You should also configure your web browser to recognise RW32B2A.EXE as a helper application.
UNIX X11Download the file RasMol26b2.tar.gz. To unpack the file, use the command
gunzip RasMol26b2.tar.gz tar -xvf RasMol26b2.tarThis should unpack the file into a directory (RasMol2) containing the RasMol2.6b2 source code, Imakefile, Makefile examples (for Unix, PC, and Mac platforms), documentation, etc. Executable files are not included. Have a look at the INSTALL file for compilation instructions. Delete the files RasMol26b2.tar.gz and RasMol26b2.tar if you wish.

Tuesday, August 19, 2008

softwares

Alignment/Similarity Search Tools
EBI- Fasta executable: Provides sequence similarity searching against nucleotide and protein databases using the Fasta programs. Fasta can be very specific when identifying long regions of low similarity especially for highly diverged sequences.Download EBI-Fasta executable via FTP
EBI-Clustal W is a general purpose multiple sequence alignment program for DNA or proteins.It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.Download EBI-Clustal W via FTP
Clustal X: Clustal X is a new windows interface for the ClustalW multiple sequence alignment program. It provides an integrated environment for performing multiple sequence and profile alignments and analysing the results. The sequence alignment is displayed in a window on the screen. A versatile coloring scheme has been incorporated allowing you to highlight conserved features in the alignment. The pull-down menus at the top of the window allow you to select all the options required for traditional multiple sequence and profile alignment. Download Clustax (Windows OS)
TIGR-MUMmer(fast alignment of large-scale DNA and protein sequences):A system for aligning whole genome sequences. Using an efficient data structure called a suffix tree, the system is able rapidly to align sequences containing millions of nucleotides. Download MUMer Via FTP
TIGR-AAT package(A tool for analyzing and annotating genomic sequences): The AAT package includes two sets of programs, one set (DPS/NAP) for comparing the query sequence with a protein database, and the other (DDS/GAP2) for comparing the query with a cDNA database (Huang et al., 1997).Download AAT package via FTP

MCIC Bioinformatics Software

Compare Alignment - Download Now
File Size:
1.757 MB
Requirements:
Windows 95/98/Me/NT/2000/XP
License:
Free
Instructions:
The .ZIP contains 3 files. Use PKUNZIP to unzip then run Setup.exe
File Type/Name:
Zip file / Compare.ZIP
ORF Extractor - Download Now
File Size:
3.245 MB
Requirements:
Windows 95/98/Me/NT/2000/XP
License:
Free
Instructions:
The .ZIP contains 4 files. Use PKUNZIP to unzip then run Setup.exe
File Type/Name:
Zip file / OrfExtra.ZIP
Hit Extractor - Download Now
File Size:
1.758 MB
Requirements:
Windows 95/98/Me/NT/2000/XP
License:
Free
Instructions:
The .ZIP contains 3 files. Use PKUNZIP to unzip then run Setup.exe. Select the Hit Extraction option when the program first opens.
File Type/Name:
Zip file / HitExtra.ZIP
Sequence Order Search - Download Now
File Size:
1.762 MB
Requirements:
Windows 95/98/Me/NT/2000/XP
License:
Free
Instructions:
The .ZIP contains 3 files. Use PKUNZIP to unzip then run Setup.exe. Select the SOS option when the program first opens.
File Type/Name:
Zip file / SOS.ZIP
PexFinder 2 - Download Now
File Size:
1.756 MB
Requirements:
Windows 95/98/Me/NT/2000/XP
License:
Free
Instructions:
The .ZIP contains 3 files. Use PKUNZIP to unzip then run Setup.exe.
File Type/Name:
Zip file / PexFind.ZIP
EleNor - Download Now
File Size:
1.799 MB
Requirements:
Windows 95/98/Me/NT/2000/XP
License:
Free
Instructions:
The .ZIP contains 3 files. Use PKUNZIP to unzip then run Setup.exe.
File Type/Name:
Zip file / EleNor.ZIP
If you have any questions about these programs contact Ian Holford at the MCIC

Sunday, August 17, 2008

Bioinformatics Algorithms - Techniques and Applications

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Bioinformatics Algorithms: Techniques and Applications
Language: English | 500 pages | Data: 2008 | PDF | size : 6 Mb


Targets the future collaboration of researchers in algorithms, bioinformatics, and molecular biology. It addresses critical bioinformatics research areas of protein-protein interaction, molecular modeling in drug design, and structural biology. Some of the most important topics in the field of bioinformatics are covered with selected topics that are gaining increased interest, including drug design, gene finding, and text mining in bioinformatics.

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Handbook of Applied Algorithms: Solving Scientific

Handbook of Applied Algorithms: Solving Scientific

Postby Octopus on Thu Jul 17, 2008 10:18 am

TITLE : Handbook of Applied Algorithms: Solving Scientific, Engineering, and Practical Problems
TYPE : Computer/Programming
AUTHOR : Amiya Nayak, Ivan Stojmenovic
PUBLISHER : Wiley-IEEE Press
ISBN : 0470044926
PAGES : 560 pages
EDITION : 1st
LANGUAGE : ENGLISH
RELEASE DATE : 07/09/2008

MAKER : Team DDU
PACKAGER : Team DDU
SUPPLIER : Team DDU
FORMAT : PDF
SIZE : 3.44 MB

RELEASE NOTES :
Discover the benefits of applying algorithms to solve scientific, engineering, and practical problems

Providing a combination of theory, algorithms, and simulations, Handbook of Applied Algorithms presents an all-encompassing treatment of applying algorithms and discrete mathematics to practical problems in "hot" application areas, such as computational biology, computational chemistry, wireless networks, and computer vision.

In eighteen self-contained chapters, this timely book explores:
* Localized algorithms that can be used in topology control for wireless ad-hoc or sensor networks
* Bioinformatics algorithms for analyzing data
* Clustering algorithms and identification of association rules in data mining
* Applications of combinatorial algorithms and graph theory in chemistry and molecular biology
* Optimizing the frequency planning of a GSM network using evolutionary algorithms
* Algorithmic solutions and advances achieved through game theory

Complete with exercises for readers to measure their comprehension of the material presented, Handbook of Applied Algorithms is a much-needed resource for researchers, practitioners, and students within computer science, life science, and engineering.

Amiya Nayak, PhD, has over seventeen years of industrial experience and is Full Professor at the School of Information Technology and Engineering at the University of Ottawa, Canada. He is on the editorial board of several journals. Dr. Nayak's research interests are in the areas of fault tolerance, distributed systems/algorithms, and mobile ad-hoc networks. Ivan StojmenoviC?, PhD, is Professor at the University of Ottawa, Canada (www.site.uottawa.ca/~ivan), and Chair Professor of Applied Computing at the University of Birmingham, United Kingdom. Dr. Stojmenovic? received the Royal Society Wolfson Research Merit Award. His current research interests are mostly in the design and analysis of algorithms for wireless ad-hoc and sensor networks.

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