3 The Bioperl-run package has (Bio)perl wrappers written for the following applications:
6 1. Coils - Prediction of Coiled Coil Regions in Proteins
8 http://www.ch.embnet.org/software/COILS_form.html
10 2. EMBOSS Applications - European Molecular Biology Open Software Suite
11 Bio::Tools::Run::EMBOSSApplication
12 http://www.hgmp.mrc.ac.uk/Software/EMBOSS/
14 3. Eponine - Transcription Start Site finder
15 Bio::Tools::Run::Eponine
16 http://www.sanger.ac.uk/Software/analysis/eponine/
18 4. FootPrinter - Program that performs phylogenetic footprinting.
19 Bio::Tools::Run::FootPrinter
20 http://abstract.cs.washington.edu/~blanchem/FootPrinterWeb/FootPrinterInput.pl
22 5. Genewise - Gene prediction program
23 Bio::Tools::Run::Genewise
24 http://www.sanger.ac.uk/software/wise2
26 6. Genscan - Identification of complete gene structures in genomic DNA
27 Bio::Tools::Run::Genscan
28 http://genes.mit.edu/GENSCAN.html
30 7. Hmmpfam - search a single sequence against an HMM database
31 Bio::Tools::Run::Hmmpfam
32 http://hmmer.wustl.edu/
34 8. PISE - Web interfaces for Biological Programs
35 Bio::Tools::Run::PiseApplication
36 http://www-alt.pasteur.fr/~letondal/Pise/
38 9. 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
42 10. 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/
46 11. 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
50 12. Pseudowise - a pseudogene precdiction program, part of the wise2 package
51 Bio::Tools::Run::Pseudowise
52 http://www.sanger.ac.uk/software/wise2
54 13. RepeatMasker - screens DNA sequences in fasta format against a library of repetitive elements
55 Bio::Tools::Run::RepeatMasker
56 http://repeatmasker.genome.washington.edu
58 14. Seg - Identify low-complexity regions in protein sequences
60 ftp://ftp.ncbi.nih.gov/pub/seg/
62 15. 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/
66 16. Tmhmm - Prediction of transmembrane helices in proteins
67 Bio::Tools::Run::Tmhmm
68 http://www.cbs.dtu.dk/services/TMHMM/
70 17. TribeMCL - Method for clustering proteins into related groups.
71 Bio::Tools::Run::TribeMCL
72 http://www.ebi.ac.uk/research/cgg/tribe/
74 19. Molphy - MOLecular PHYlogenetics Package
75 Bio::Tools::Run::Molphy
76 http://www.ism.ac.jp/software/ismlib/softother.e.html
78 20. Phylip - Suite of Phylogenetics programs (Version 3.6)
79 Bio::Tools::Run::Phylip
80 http://evolution.genetics.washington.edu/phylip.html
82 22. DBA - DNA Block Aligner
83 Bio::Tools::Run::Alignment::DBA
84 http://www.sanger.ac.uk/software/wise2
86 23. Sim4 - Align CDNA to genomic sequences
87 Bio::Tools::Run::Alignment::Sim4
88 http://globin.cse.psu.edu/
90 25. BLAST - Basic Local Alignment Search Tool
91 Bio::Tools::Run::StandAloneBlast (in bioperl-live CVS repository)
92 ftp://ftp.ncbi.nih.gov/blast/executables
94 26. FASTA,SSEARCH - Pairwise sequence alignment
95 Bio::Tools::Run::StandAloneFasta
96 ftp://ftp.virginia.edu/pub/fasta
98 27. Promoterwise - Sequence alignment designed
99 for promoter sequences
100 http://www.sanger.ac.uk/software/wise2
102 28. Lagan - Lagan suite of tools including MLAGAN
103 http://lagan.stanford.edu/
105 29. Vista - Visualizing global DNA sequence alignments of arbitrary length
106 http://www-gsd.lbl.gov/vista/VISTAdownload2.html
108 30. Exonerate - A package of alignment tools for protein and EST to genome/DNA alignments
109 http://www.ebi.ac.uk/~guy/exonerate/
111 31. AMAP- Protein multiple alignment based sequence annealing
112 http://bio.math.berkeley.edu/amap/
114 32. Blat - An alignment tool like BLAST, but structured differently
115 http://genome.ucsc.edu/cgi-bin/hgBlat