[Bioperl-l] genbank (blast) alignments
Chris Fields
cjfields at illinois.edu
Thu Jul 23 22:53:29 UTC 2009
Lots of emails to answer, so little time. Doesn't help when my VPN
goes out either ;>
What you want appears to be generating a multiple alignment from
pairwise alignment. The answer is 'very likely not'. However, the
local BLAST executable does have several options for generating
alignments from HSP data (assuming that's what you mean):
-m : alignment view options:
0 = pairwise,
1 = query-anchored showing identities,
2 = query-anchored no identities,
3 = flat query-anchored, show identities,
4 = flat query-anchored, no identities,
5 = query-anchored no identities and blunt ends,
6 = flat query-anchored, no identities and blunt ends,
7 = XML Blast output,
8 = tabular,
9 tabular with comment lines [Integer] default = 0
You can set this by reformatting on the BLAST web site (here's a chunk
of the output, note the query):
Query 61 PVTVGEIDITLYRDDLS-KKTSND-E--PLVKGADIPVDIT-------
DQKVILVDDVLY 109
NP_389430 61 PVTVGEIDITLYRDDLS-KKTSND-E--PLVKGADIPVDIT-------
DQKVILVDDVLY 109
YP_001421124 61 PVTVGEIDITLYRDDLT-KKTSNE-E--PLVKGADIPADIT-------
DQKVIVVDDVLY 109
YP_078940 63 KVTVGELDITLYRDDLS-KKTSNK-E--PLVKGADIPADIT-------
DQKVILVDDVLY 111
ZP_03053294 61 PVIVGELDITLYRDDLT-KKTENQ-D--PLVKGADIPADIN-------
DKTLIVVDDVLF 109
YP_001486689 61 PVIVGELDITLYRDDLT-KKTDNQ-D--PLVKGADIPADIN-------
DKTLIVVDDVLF 109
YP_002949168 60 AVPVGELDITLYRDDLT-VKTIDH-E--PLVKGTDVPFDVT-------
NKKVILVDDVLF 108
ZP_01860800 61 KMPVGEIDITLYRDDLT-VKTANE-E--PEVKGSDLPVDVT-------
DKKVILIDDVLF 109
ZP_04121773 61 EMEVGELDITLYRDDLT-LQSKNK-E--PLVKGSDIPVDIT-------
KKKVILVDDVLY 109
ZP_04218628 61 EMEVGELDITLYRDDLT-LQSKNK-E--PLVKGSDIPVDIT-------
KKKVILVDDVLY 109
YP_002316154 66 SIPVGELDITLYRDDLT-VKTDDR-E--PLVKGTDVPFSVT-------
NQKVILVDDVLF 114
ZP_00240953 61 EMEVGELDITLYRDDLT-LQSKNE-E--PLVKGSDIPVDIT-------
KKKVILVDDVLY 109
YP_037953 61 EIEVGELDITLYRDDLT-LQSKNK-E--PLVKGSDIPVDIT-------
KKKVILVDDVLY 109
ZP_04193166 61 KMEVGELDITLYRDDLT-LQSKNK-E--PLVKGSDIPVDIT-------
KKKVILVDDVLY 109
NP_833611 61 EMEVGELDITLYRDDLT-LQSKNK-E--PLVKGSDIPVDIT-------
KKKVILVDDVLY 109
ZP_03018932 61 EMEVGELDITLYRDDLT-LQSKNK-E--PLVKGSDIPVDIT-------
KKKVILVDDVLY 109
...
We do not have a parser for that format, BTW, but it wouldn't be too
hard to get something working quickly based on one of the current
parsers. Probably could go AlignIO or SearchIO (or both).
chris
On Jul 23, 2009, at 2:38 PM, Robert Buels wrote:
> Wow, that silence is deafening. I can't believe somebody who knows
> what they're talking about hasn't written you back yet.
>
> Perhaps you could do some kind of transformation where you read in
> the BLAST report with Bio::SearchIO, and then write to MSF with
> Bio::AlignIO::msf? You would probably need to do some fiddling to
> create the proper objects and relationships that Bio::AlignIO::msf
> would want.
>
> But this reply probably isn't helpful, because you probably already
> knew that much. I'm mostly just trying to add to this thread so
> that people who actually know a lot about BioPerl's functions in
> this area will see it and hopefully be of more help.
>
> Rob
>
> --
> Robert Buels
> Bioinformatics Analyst, Sol Genomics Network
> Boyce Thompson Institute for Plant Research
> Tower Rd
> Ithaca, NY 14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu
>
>
> Thomas Keller wrote:
>> Greetings,
>> Blast 2.2.21 has a multi-sequence alignment feature that is really
>> handy: put in the accession number of the refseq in one sequence
>> field and a concatenated fasta file of the Sanger reads to align in
>> the second box and it does the alignments. Unfortunately, the
>> output is a series of alignments rather than the more useful msf
>> format with all reads aligned with the reference.
>> Is there a bioperl module that reads the blast alignments and
>> converts it to an msf alignment?
>> thanks,
>> Tom
>> kellert at ohsu.edu
>> 503-494-2442
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
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>
>
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