SB Transmembrane domains - mendessoares/BuddySuite GitHub Wiki
--transmembrane_domains, -tmd
This feature will be released with V1.2. Currently available in the development branch of the git repo.
Description
Annotate transmembrane domains using the TOPCONS2 web service. The input sequences are transmitted to the server, so an active internet connection is required, and the results are downloaded and processed into new annotations.
Processing can take some time, so SeqBuddy prints its current status to the terminal to let you know it's still alive and waiting. This can be suppressed with the -q flag.
TOPCONS2 generates many data files which are generally discarded by SeqBuddy after your processed sequences are returned. Use the -k flag to retain these files.
If the input sequence is in a format that does not support rich annotation, then the output will be converted to the genbank format (this can be over-ridden with the -o flag).
Argument
Job ID ( str )
Optional. Specify one or more TOPCONS job IDs that have previously been submitted via SeqBuddy using the same computer. To prevent any weird sequence names from breaking the run, they are all hashed before being uploaded to the server. A 'hash map' is saved in the BuddySuite config directory so you can retrieve previous jobs and decode the sequence names, but these hash maps will not be available to instances of SeqBuddy on other computers.
Example
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 example 1
$: sb Mle-Panxα2.gb -tmd
Output
Job 'rst_AZGyW4' submitted
************** Complete **************
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)
/created_by="User"
/label=""
/modified_by="User"
splice_donor 298..307
/created_by="User"
/label="Donor"
splice_acceptor complement(495..504)
/created_by="User"
/label="Acceptor"
TMD1 82..147
TMD2 418..486
TMD3 676..744
TMD4 937..1032
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 example 2
Retrieve a previous run. Note that you still need to specify the input sequences.
$: sb Mle-Panxα2.gb -tmd rst_AZGyW4
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)
/created_by="User"
/label=""
/modified_by="User"
splice_donor 298..307
/created_by="User"
/label="Donor"
splice_acceptor complement(495..504)
/created_by="User"
/label="Acceptor"
TMD1 82..147
TMD2 418..486
TMD3 676..744
TMD4 937..1032
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
//