SB Prosite scan

--prosite_scan, -psc

Implemented in version 1.2 (deprecated server), updated in version 1.3

Description

Annotate a DNA, RNA, or protein sequence using EMBL-EBI's implementation of PROSITE (i.e., searching against the PROSITE-profiles database).

NOTE: Internet connection required

Examples

Usage example 1

Protein sequence. In this case, a FASTA file is being passed in; this will be converted to genbank for output unless you specifically set the output flag (-o).

Input file: Mle-Panxα4.fa

>Mle-Panxα4 cDNA and genomic - ML129317a.
mviellagykglspfkdatvddswdqinrcyvfiamvvmgavttmrqysgtliacdgftk
fhpqfaedycwsigmytvreaydlpssmvaypgvipwdmpacvprllkngtrtkcgsekd
vmpsekiyhlwyqwasfyfwivailyyapyimfkqlgggeykplikllclasgspeqqmq
diqervvkwlffrfktyifakgyyawlrknsfsiaigvtklsyllitilvfyltgfmfey
gsntwyrygadwygtrfssyhetnnsitltkdiifpkmvaceikrwgpsgievetaqcvl
apnvlyqylflftwylliavfftnliscflhisemffsngtynrmidqgmlpdkpsyryv
fmnigaggreivqiltdnsnpllfskifddltnllittsknadvienlskldssvielgs
kdsi*

Usage

$ sb Mle-Panxα4.fa -psc

Output

LOCUS       Mle-Panxα4               425 aa                     UNK 01-JAN-1980
DEFINITION  cDNA and genomic - ML129317a..
ACCESSION   Mle-Panxα4
VERSION     Mle-Panxα4
KEYWORDS    .
SOURCE      .
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     Region          16..401
                     /note="Innexin"
ORIGIN
        1 mviellagyk glspfkdatv ddswdqinrc yvfiamvvmg avttmrqysg tliacdgftk
       61 fhpqfaedyc wsigmytvre aydlpssmva ypgvipwdmp acvprllkng trtkcgsekd
      121 vmpsekiyhl wyqwasfyfw ivailyyapy imfkqlggge ykplikllcl asgspeqqmq
      181 diqervvkwl ffrfktyifa kgyyawlrkn sfsiaigvtk lsyllitilv fyltgfmfey
      241 gsntwyryga dwygtrfssy hetnnsitlt kdiifpkmva ceikrwgpsg ievetaqcvl
      301 apnvlyqylf lftwylliav fftnliscfl hisemffsng tynrmidqgm lpdkpsyryv
      361 fmnigaggre ivqiltdnsn pllfskifdd ltnllittsk nadvienlsk ldssvielgs
      421 kdsi*
//

Usage example 2

DNA sequence.

Input file: Mle-Panxα2.gb

LOCUS       Mle-Panxα2              1314 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25998a.
ACCESSION   Mle-Panxα2
VERSION     Mle-Panxα2
KEYWORDS    .
SOURCE
  ORGANISM  . . .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..144,145..307,308..555,556..688,689..810,811..1314)
                     /modified_by="User"
                     /created_by="User"
                     /label
     splice_donor    298..307
                     /created_by="User"
                     /label="Donor"
     splice_acceptor complement(495..504)
                     /created_by="User"
                     /label="Acceptor"
ORIGIN
        1 atggtattgg atctcatttc tggaagcttg aatggctttt taaagatcaa gtcagttagc
       61 atcgacgatc agtgggacca gattaacaga acctatttgg tcatgttttg tattttatct
      121 ggtacaatca tgacctttaa acagaattta ggatcaataa tacactgtat atcggatgca
      181 agaggcgacg acagttcgtt tgcggatgct catgcgacat ttgtgcaaga ctattgtgct
      241 gctcaagggc tgtacacttt aaaagaagtg tatgacaagt cttggccaga tgaaattcct
      301 tacccaggta ttctccaaat gaaaacaatc ggttgtttcc cggggagaca gttcaaaaac
      361 ggaaccccca tccagtgccc ggacgagaaa gatctgaaac ccttcacaac ggtctatcat
      421 gtctggtaca tgttcgtacc gttctacttc tgcgctgttg gcatcgcttt ttacttcccc
      481 tacacggttt tcagacacct cagcggcatc tacgacatca agcctatgtt gaacagcctt
      541 gccctcgaca ttggggccta cacggaggag gacataagtc gacgtataga caatgtctcg
      601 aggtggttgt acatcaagtt ggatccctac atgaacaaca tgcttcctta tactcagata
      661 gttcacaaac attccatctt ttacacggtg atgttggtga aggtgatgta cctagctacc
      721 agtgtttcta ttttttacgc cactcaccgg atattcgacc aaggaaactt tgcactctac
      781 ggatacgatg ttctaatgag cataccacag gaaacaagct ataaagtgat ggacacaatc
      841 ttccctaaaa tggttggctg tgagatcaac atgtggggcc ggactggcga acagagcgaa
      901 tctcttctgt gtgtcctccc tcaaaacatc ggcaaccaat acttcttcct tatattctgg
      961 tttctcctga ttctcaccat actttccaac tgtatctctg taatagtgac catattcaga
     1021 tttatattcg ttagtgggag ctacaaaagg ttcctggcta ccagcctctt gaatcacgaa
     1081 gaacgataca agctggtgtt tacacatgtc ggcacgactg gaagatacat tttactgctc
     1141 tgtgccgatc atagcaaccc caaaatattc gaggatcttc tagagatcgt ctgttccctt
     1201 ctcatagcaa actatcacaa aagaaagagg agtcgggata agggacacag tcgagcggag
     1261 ggggtaggga ctaaagggcg acacggtctg tcttttgtgg actcaaccgt gtga
//

Usage

$ sb Mle-Panxα2.gb -psc

Output

LOCUS       Mle-Panxα2              1314 bp    DNA              UNA 02-JAN-2015
DEFINITION  cDNA - ML25998a.
ACCESSION   Mle-Panxα2
VERSION     Mle-Panxα2
KEYWORDS    .
SOURCE
  ORGANISM  .
            .
FEATURES             Location/Qualifiers
     CDS             order(1..144,145..307,308..555,556..688,689..810,811..1314)
                     /modified_by="User"
                     /created_by="User"
                     /label=""
     splice_donor    298..307
                     /created_by="User"
                     /label="Donor"
     splice_acceptor complement(495..504)
                     /created_by="User"
                     /label="Acceptor"
     Region          49..1221
                     /note="Innexin"
ORIGIN
        1 atggtattgg atctcatttc tggaagcttg aatggctttt taaagatcaa gtcagttagc
       61 atcgacgatc agtgggacca gattaacaga acctatttgg tcatgttttg tattttatct
      121 ggtacaatca tgacctttaa acagaattta ggatcaataa tacactgtat atcggatgca
      181 agaggcgacg acagttcgtt tgcggatgct catgcgacat ttgtgcaaga ctattgtgct
      241 gctcaagggc tgtacacttt aaaagaagtg tatgacaagt cttggccaga tgaaattcct
      301 tacccaggta ttctccaaat gaaaacaatc ggttgtttcc cggggagaca gttcaaaaac
      361 ggaaccccca tccagtgccc ggacgagaaa gatctgaaac ccttcacaac ggtctatcat
      421 gtctggtaca tgttcgtacc gttctacttc tgcgctgttg gcatcgcttt ttacttcccc
      481 tacacggttt tcagacacct cagcggcatc tacgacatca agcctatgtt gaacagcctt
      541 gccctcgaca ttggggccta cacggaggag gacataagtc gacgtataga caatgtctcg
      601 aggtggttgt acatcaagtt ggatccctac atgaacaaca tgcttcctta tactcagata
      661 gttcacaaac attccatctt ttacacggtg atgttggtga aggtgatgta cctagctacc
      721 agtgtttcta ttttttacgc cactcaccgg atattcgacc aaggaaactt tgcactctac
      781 ggatacgatg ttctaatgag cataccacag gaaacaagct ataaagtgat ggacacaatc
      841 ttccctaaaa tggttggctg tgagatcaac atgtggggcc ggactggcga acagagcgaa
      901 tctcttctgt gtgtcctccc tcaaaacatc ggcaaccaat acttcttcct tatattctgg
      961 tttctcctga ttctcaccat actttccaac tgtatctctg taatagtgac catattcaga
     1021 tttatattcg ttagtgggag ctacaaaagg ttcctggcta ccagcctctt gaatcacgaa
     1081 gaacgataca agctggtgtt tacacatgtc ggcacgactg gaagatacat tttactgctc
     1141 tgtgccgatc atagcaaccc caaaatattc gaggatcttc tagagatcgt ctgttccctt
     1201 ctcatagcaa actatcacaa aagaaagagg agtcgggata agggacacag tcgagcggag
     1261 ggggtaggga ctaaagggcg acacggtctg tcttttgtgg actcaaccgt gtga
//