* indicates proprietary methods
Data Sources
origin last updated descr url
CCDS/Human 2008-05-23 "human protein coding regions that are consistently annotated and of high quality" http://www.ncbi.nlm.nih.gov/CCDS/
CCDS/Mouse 2008-05-23 mouse protein coding regions that are consistently annotated and of high quality http://www.ncbi.nlm.nih.gov/CCDS/
Cosmic 2008-04-01 cosmic protein sequences http://www.sanger.ac.uk/genetics/CGP/cosmic/
Ensembl/Chimp 2009-08-13 Ensembl chimp sequences http://www.ensembl.org/Pan_troglodytes
Ensembl/Chimp (ab initio) 2009-08-13 Ensembl chimp sequences -- ab initio sequences http://www.ensembl.org/Pan_troglodytes
Ensembl/Cow 2009-08-13 Ensembl cow sequences http://www.ensembl.org/Bos_taurus
Ensembl/Cow (ab initio) 2009-08-13 Ensembl cow sequences -- ab initio sequences http://www.ensembl.org/Bos_taurus
Ensembl/Fly 2009-08-13 Ensembl drosophila sequences http://www.ensembl.org/Drosophila_melanogaster
Ensembl/Fly (ab initio) 2009-08-13 Ensembl drosophila sequences -- ab initio sequences http://www.ensembl.org/Drosophila_melanogaster
Ensembl/Human 2009-08-13 Ensembl protein sequences http://www.ensembl.org/Homo_sapiens
Ensembl/Human (ab initio) 2009-08-13 Ensembl protein sequences -- ab initio sequences http://www.ensembl.org/Homo_sapiens
Ensembl/Mouse 2009-08-13 Ensembl mouse sequences http://www.ensembl.org/Mus_musculus
Ensembl/Mouse (ab initio) 2009-08-13 Ensembl mouse sequences -- ab initio sequences http://www.ensembl.org/Mus_musculus
Ensembl/Rat 2009-08-13 Ensembl rat sequences http://www.ensembl.org/Rattus_norvegicus
Ensembl/Rat (ab initio) 2009-08-13 Ensembl rat sequences -- ab initio sequences http://www.ensembl.org/Rattus_norvegicus
Ensembl/Zebrafish 2009-08-13 Ensembl zebrafish sequences http://www.ensembl.org/Danio_rerio
Ensembl/Zebrafish (ab initio) 2009-08-13 Ensembl zebrafish sequences -- ab initio sequences http://www.ensembl.org/Danio_rerio
FANTOM Functional Annotation of Mouse http://fantom.gsc.riken.go.jp/
HUGE 2005-09-15 http://www.kazusa.or.jp/huge/
IPI 2003-08-20 International Protein Index http://www.ebi.ac.uk/IPI/
MD5 MD5 checksum
MGC/Human Mammalian Gene Collection (NIH) -- Human http://mgc.nci.nih.gov/
MGC/Mouse Mammalian Gene Collection (NIH) -- Mouse http://mgc.nci.nih.gov/
pataa 2008-06-15 NCBI Patent Database ftp://ftp.ncbi.nih.gov/blast/db
PDB 2009-08-24 Protein Data Bank (aka RCSB) http://www.rcsb.org/
RefSeq 2009-08-26 NCBI Reference Sequence database http://www.ncbi.nlm.nih.gov/RefSeq/
ROUGE 2005-09-15 http://www.kazusa.or.jp/rouge/
RPS Riken Representative Protein Set http://www.genome.org/cgi/content/full/13/6b/1350
STRING 2008-05-21 database of known and predicted protein-protein interactions http://string.embl.de/
UniProtKB/Swiss-Prot 2009-08-13 "fully annotated records which include curator-evalutated computational analysis" http://www.uniprot.org/
UniProtKB/TrEMBL 2009-08-14 "[UniProt] records awaiting manual curation" http://www.uniprot.org/
Unison 2003-07-08 Unison annotations http://www.unison-db.org/
Execution Parameters
params_id name descr commandline
19 BIG-PI default BIG-PI GPI prediction; [PubMed] bigpi metazoa %s short
61 BLAST BLAST based alignments with 50%id and 50 hsp len cutoff run-papseq -FF -z10000000 -e 1e-20 --hl 50 --pi 50 -b 10000
41 dispro http://www.ics.uci.edu/~baldig/dispro.html MANUAL
39 disprot VL3H disprot protein disorder prediction -- http://www.ist.temple.edu/disprot/predictor.php MANUAL: temple-disprot.pl
4 EMBOSS/antigenic antigenicity predictions; http://emboss.sourceforge.net/apps/antigenic.html antigenic -minlen 6 -rformat simple
37 EMBOSS/pepcoil EMBOSS pepcoil coiled-coil predictions pepcoil -noother -window 28 -filter
5 EMBOSS/sigcleave signal cleavage prediction; http://emboss.sourceforge.net/apps/sigcleave.html sigcleave -minweight 3.5 -rformat simple
11 Genome BLAT genomic localization of protein sequences; http://genome.ucsc.edu/cgi-bin/hgBlat gfClient -t=dnax -q=prot trp 17701 /usr/seqdb2_nb/blat/nhgd
55 hmmer standard HMMer runs against a large database ldhmmpfam --acc -E10 -Z10000
59 netphos 3.1 S,T,Y phosphorylation predictions /gne/research/apps/netphos/3.1/x86_64-linux-2.6/bin/netphos
48 PMAP 2006-12-08 genomic localization of protein sequences pmap.2006-12-08 -d NHGD_R36 -B 2 -f 0 -t 3 %s
63 protcomp p8 Protcomp protein localization /gne/research/apps/protcomp/protcompp8/x86_64-linux-2.6/protcomp
17 Psipred v2.45 PSIPRED secondary structure prediction; [PubMed] runpsipred -j 3 -h 0.001 -a 2 -s 1 -hb 1 -sb 1 -d nr-2004-12-21-pfilter
8 PSSM default
12 regexp
47 seg segment sequence(s) by local complexity seg %s 12 2.2 2.5 -l
28 SignalP 3.0 (euk) Signal sequence prediction per [PubMed] /gne/research/apps/signalp/signalp-3.0/i686-linux-2.6/signalp -t euk -f summary
9 tmdetect default Genentech in-house TM detection; superseded by TMHMM tmdetect
29 TMHMM 2.0c TMHMM 2.0c, http://www.cbs.dtu.dk/services/TMHMM/ /gne/research/apps/TMHMM/TMHMM2.0c/i686-linux-2.6/bin/tmhmm --short
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