Question: Convert Blast Table With Hsps To Alignment
0
gravatar for Empyrean
8.2 years ago by
Empyrean160
Empyrean160 wrote:

Hello

I have the following BLAST table format output:

GRMZM2G5555   GRMZM2G5555   100.00  5197    0       0       2886    8082    2886    8082    0.0     9880
GRMZM2G5555   GRMZM2G5555   100.00  1418    0       0       1       1418    1       1418    0.0     2769
GRMZM2G5555   GRMZM2G5555   100.00  1377    0       0       1445    2821    1445    2821    0.0     2688
GRMZM2G5555   GRMZM2G3333   99.13   1268    9       2       1445    2711    759     2025    0.0     2369
GRMZM2G5555   GRMZM2G3333   99.17   724     6       0       687     1410    1       724     0.0     1388
GRMZM2G5555   GRMZM2G2222   95.73   1310    23      8       4045    5333    647     1944    0.0     2068
GRMZM2G5555   GRMZM2G1111   96.41   668     15      5       4677    5342    8063    7403    0.0     1031
GRMZM2G5555   GRMZM2G1111   95.52   67      3       0       5428    5494    3703    3637    1e-21    109

I ran BLAST on a FASTA file against the same FASTA file. So the first hit will be itself. Now the BLAST output is providing several different HSPs. But I wanted all the HSPs to be combined and display as one, so that I can find the whole coverage of subject on query. Can anyone suggest me how to achieve this or a place to find the scripts for this problem.

thanks

format alignment blast • 3.0k views
ADD COMMENTlink modified 8.2 years ago by Marina Manrique1.3k • written 8.2 years ago by Empyrean160
1

futher give example of hsp output you want!

ADD REPLYlink written 8.2 years ago by Thaman3.2k
1
gravatar for Michael Schubert
8.2 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

BLAST stands for Basic Local Alignment Search Tool, which is exactly what it does: searching for local alignments between two sequences.

What you seem to want is a global alignment. There are many tools available that do that for you, however, BLAST is not one of them.

I suggest you get the sequence IDs from your file and use e.g. CLUSTALW, MUSCLE, or T-COFFEE to globally align them.

ADD COMMENTlink written 8.2 years ago by Michael Schubert6.9k
1
gravatar for Casey Bergman
8.2 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

To answer your question (but not your title) I suggest using BLAT, which automatically chains HSPs from the same target as part of its PSL format.

ADD COMMENTlink written 8.2 years ago by Casey Bergman18k
1
gravatar for Marina Manrique
8.1 years ago by
Marina Manrique1.3k
Granada
Marina Manrique1.3k wrote:

Maybe you could try with the pairwise format instead (flag -m 0 I think). I think that in this format all the HSPs that make up a hit are all represented together so you'd need only to look at the query start position and end position to get the whole coverage.

Anyway, if you don't mind to use Java and XML format, I'd recommend to take a look at this Java project: Era7BioinfoXML It's got a set of XML wrapper classes based on Jdom library. In particular the class Hsp.java is a model of the HSP element, using the methods getQueryFrom and getQueryTo you can get the positions and thus calculate the coverage.

Here you are a sample of the pairwise format [?][?] BLASTP 2.0.9 [May-07-1999]

Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402.

Query= X52524 LOCUS PFEBA175_1 (501 letters)

Database: swissprot 80,000 sequences; 29,085,965 total letters

Searching.................................................done

                                                               Score     E

Sequences producing significant alignments: (bits) Value

SWISSPROT:EBA1_PLAFC P19214 plasmodium falciparum (isolate camp... 950 0.0 SWISSPROT:PVDB_PLAKN P50493 plasmodium knowlesi. duffy receptor... 96 1e-19 SWISSPROT:PVDR_PLAVI P22290 plasmodium vivax. duffy receptor pr... 96 1e-19 SWISSPROT:PVDG_PLAKN P50494 plasmodium knowlesi. duffy receptor... 95 2e-19 SWISSPROT:PVDA_PLAKN P22545 plasmodium knowlesi. duffy receptor... 83 8e-16 SWISSPROT:SCP1_RAT Q03410 rattus norvegicus (rat). synaptonemal... 46 1e-04 SWISSPROT:SCP1_MOUSE Q62209 mus musculus (mouse). synaptonemal ... 43 0.001

SWISSPROT:EBA1_PLAFC P19214 plasmodium falciparum (isolate camp / malaysia). erythrocyte-binding antigen eba-175. 2/1996 Length = 1435

Score = 950 bits (2430), Expect = 0.0 Identities = 461/501 (92%), Positives = 461/501 (92%)

Query: 1 NIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDY 60 NIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDY Sbjct: 500 NIDRIYDKNLLMIKEHILAIAIYESRILKRKYKNKDDKEVCKIINKTFADIRDIIGGTDY 559

Query: 61 WNDLSNRKLVGKINTNSKYVHRNKKNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDD 120 WNDLSNRKLVGKINTNSKYVHRNKKNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDD Sbjct: 560 WNDLSNRKLVGKINTNSKYVHRNKKNDKLFRDEWWKVIKKDVWNVISWVFKDKTVCKEDD 619

Query: 121 IENIPQFFRWFSEWGDDYCQDKTKMIETLKVECKEKPCEDDNCKSKCNSYKEWISKKKEE 180 IENIPQFFRWFSEWGDDYCQDKTKMIETLKVECKEKPCEDDNCKSKCNSYKEWISKKKEE Sbjct: 620 IENIPQFFRWFSEWGDDYCQDKTKMIETLKVECKEKPCEDDNCKSKCNSYKEWISKKKEE 679

Query: 181 YNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKC 240 YNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKC Sbjct: 680 YNKQAKQYQEYQKGNNYKMYSEFKSIKPEVYLKKYSEKCSNLNFEDEFKEELHSDYKNKC 739

Query: 241 TMCPEVKDVPISIIRNNEQTSQEAVPEENTEIAHRTETPSISEGPKGNEQKERDDDSLSK 300 TMCPEVKDVPISIIRNNEQTSQEAVPEENTEIAHRTETPSISEGPKGNEQKERDDDSLSK Sbjct: 740 TMCPEVKDVPISIIRNNEQTSQEAVPEENTEIAHRTETPSISEGPKGNEQKERDDDSLSK 799

Query: 301 ISVSPENSRPETDAKDTSNLLKLKGDVDISMPKAVIGSSPNDNINVTEQGDNISGVNSKP 360 ISVSPENSRPETDAKDTSNLLKLKGDVDISMPKAVIGSSPNDNINVTEQGDNISGVNSKP Sbjct: 800 ISVSPENSRPETDAKDTSNLLKLKGDVDISMPKAVIGSSPNDNINVTEQGDNISGVNSKP 859

Query: 361 LSDDVRPDKKELEDQNSDESEETVVNHISKSPSIXXXXXXXXXXXXXXXXXXXXXXXXID 420 LSDDVRPDKKELEDQNSDESEETVVNHISKSPSI ID Sbjct: 860 LSDDVRPDKKELEDQNSDESEETVVNHISKSPSINNGDDSGSGSATVSESSSSNTGLSID 919

Query: 421 DDRNGDTFVRTQDTANTEDVIRXXXXXXXXXXXXXXXXRHSTSESLSSPEEKMLTDNEGG 480 DDRNGDTFVRTQDTANTEDVIR RHSTSESLSSPEEKMLTDNEGG Sbjct: 920 DDRNGDTFVRTQDTANTEDVIRKENADKDEDEKGADEERHSTSESLSSPEEKMLTDNEGG 979

Query: 481 NSLNHEEVKEHTSNSDNVQQS 501 NSLNHEEVKEHTSNSDNVQQS Sbjct: 980 NSLNHEEVKEHTSNSDNVQQS 1000 [?][?]

HTH,

Marina

ADD COMMENTlink written 8.1 years ago by Marina Manrique1.3k
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