1INSTALL.PROGRAMS: 2 3The Bioperl-run package has (Bio)perl wrappers written for the following applications: 4 5 61. Coils - Prediction of Coiled Coil Regions in Proteins 7 Bio::Tools::Run::Coil 8 http://www.ch.embnet.org/software/COILS_form.html 9 102. EMBOSS Applications - European Molecular Biology Open Software Suite 11 Bio::Tools::Run::EMBOSSApplication 12 http://www.hgmp.mrc.ac.uk/Software/EMBOSS/ 13 143. Eponine - Transcription Start Site finder 15 Bio::Tools::Run::Eponine 16 http://www.sanger.ac.uk/Software/analysis/eponine/ 17 184. FootPrinter - Program that performs phylogenetic footprinting. 19 Bio::Tools::Run::FootPrinter 20 http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl 21 225. Genewise - Gene prediction program 23 Bio::Tools::Run::Genewise 24 http://www.sanger.ac.uk/software/wise2 25 266. Genscan - Identification of complete gene structures in genomic DNA 27 Bio::Tools::Run::Genscan 28 http://genes.mit.edu/GENSCAN.html 29 307. Hmmpfam - search a single sequence against an HMM database 31 Bio::Tools::Run::Hmmpfam 32 http://hmmer.wustl.edu/ 33 348. PISE - Web interfaces for Biological Programs 35 Bio::Tools::Run::PiseApplication 36 http://www-alt.pasteur.fr/~letondal/Pise/ 37 389. Primate - Near exact match finder for short sequence tags. 39 Bio::Tools::Run:::Primate 40 http://cvsweb.sanger.ac.uk/cgi-bin/cvsweb.cgi/ensembl-nci/?cvsroot=Ensembl 41 4210. FingerPRINTScan - identify the closest matching PRINTS sequence motif fingerprints in a protein sequence 43 Bio::Tools::Run::Prints 44 http://www.bioinf.man.ac.uk/fingerPRINTScan/ 45 4611. pfscan - scan a protein or DNA sequence with a profile library 47 Bio::Tools::Run::Profile 48 http://www.isrec.isb-sib.ch/software/software.html 49 5012. Pseudowise - a pseudogene precdiction program, part of the wise2 package 51 Bio::Tools::Run::Pseudowise 52 http://www.sanger.ac.uk/software/wise2 53 5413. RepeatMasker - screens DNA sequences in fasta format against a library of repetitive elements 55 Bio::Tools::Run::RepeatMasker 56 http://repeatmasker.genome.washington.edu 57 5814. Seg - Identify low-complexity regions in protein sequences 59 Bio::Tools::Run::Seg 60 ftp://ftp.ncbi.nih.gov/pub/seg/ 61 6215. Signalp - predicts the presence and location of signal peptide cleavage sites in amino acid sequences 63 Bio::Tools::Run::Signalp 64 http://www.cbs.dtu.dk/services/SignalP/ 65 6616. Tmhmm - Prediction of transmembrane helices in proteins 67 Bio::Tools::Run::Tmhmm 68 http://www.cbs.dtu.dk/services/TMHMM/ 69 7017. TribeMCL - Method for clustering proteins into related groups. 71 Bio::Tools::Run::TribeMCL 72 http://www.ebi.ac.uk/research/cgg/tribe/ 73 7419. Molphy - MOLecular PHYlogenetics Package 75 Bio::Tools::Run::Molphy 76 http://www.ism.ac.jp/software/ismlib/softother.e.html 77 7820. Phylip - Suite of Phylogenetics programs (Version 3.6) 79 Bio::Tools::Run::Phylip 80 http://evolution.genetics.washington.edu/phylip.html 81 8222. DBA - DNA Block Aligner 83 Bio::Tools::Run::Alignment::DBA 84 http://www.sanger.ac.uk/software/wise2 85 8623. Sim4 - Align CDNA to genomic sequences 87 Bio::Tools::Run::Alignment::Sim4 88 http://globin.cse.psu.edu/ 89 9025. BLAST - Basic Local Alignment Search Tool 91 Bio::Tools::Run::StandAloneBlast (in bioperl-live CVS repository) 92 ftp://ftp.ncbi.nih.gov/blast/executables 93 9426. FASTA,SSEARCH - Pairwise sequence alignment 95 Bio::Tools::Run::StandAloneFasta 96 ftp://ftp.virginia.edu/pub/fasta 97 9827. Promoterwise - Sequence alignment designed 99 for promoter sequences 100 http://www.sanger.ac.uk/software/wise2 101 10228. Lagan - Lagan suite of tools including MLAGAN 103 http://lagan.stanford.edu/ 104 10529. Vista - Visualizing global DNA sequence alignments of arbitrary length 106 http://www-gsd.lbl.gov/vista/VISTAdownload2.html 107 10830. Exonerate - A package of alignment tools for protein and EST to genome/DNA alignments 109 http://www.ebi.ac.uk/~guy/exonerate/ 110 11131. AMAP- Protein multiple alignment based sequence annealing 112 http://bio.math.berkeley.edu/amap/ 113 11432. Blat - An alignment tool like BLAST, but structured differently 115 http://genome.ucsc.edu/cgi-bin/hgBlat 116 117 118