blast results

nitinkumar · 05-11-2011, 05:17 PM

I want to edit a blast file in such way that if the query sequence has a gap, that should also comes in the reference sequence like if blast output shows:

query: aa-gcaa
|| ||||
reference: aatgcaa
and I want to remove the t from reference and place a gap...

query: aa-gcaa
|| ||||
reference: aa-gcaa

maubp · 05-12-2011, 04:19 AM

Why?

Do you know any programming languages such as Perl, Python, Ruby, Java, etc? If so have a look at BioPerl, Biopython, BioRuby, BioJava etc for libraries to work with BLAST files.

nitinkumar · 05-12-2011, 09:15 AM

Yes I have tried bioperl. but I am not able to do that. I can extract the fasta sequences from these files only..

A_Morozov · 05-15-2011, 08:38 PM

Why not use regexps for, say, finding gap-containing piece of query sequence (20 bp or so) in reference and then removing whatever you want from it?

tomc · 05-16-2011, 12:21 AM

you want to copy your query over your reference...?

If so, why not just pull you query sequence and use those,
they already have the gaps you seem to be looking for.

But it does sound odd, maybe a better explanation of why would help.

A_Morozov · 05-16-2011, 01:43 AM

Just taking a query won't work, because it can have different nucleotides (but not gaps) at some sites. After some thinking I see that you don't need any regexps, all you need is like

{
reference[i]='-' if query[i]='-';
}

for each position in sequences. Hope you can grab some sequences, dude.
But yes, I'd like to know why he would want to do something like this.

nitinkumar · 05-16-2011, 04:28 AM

Thanks for the reply and I am getting these results because of 454 sequencing errors, the query sequence is the gene of rhizobium bacteria and the subject is the sequence from matching contigs. I want to remove these sequencing errors in contigs. So that I can make the phylogeny of the contigs.

A_Morozov · 05-16-2011, 05:17 AM

But so you lose actual indels that could happen between these two species, don't you? I think that first you should make sure that this particular nucleotide is indeed an error. Maybe, it is of quality much less than of other nearby nucleotides, or it is at long repeat like aaaaaaaaa or something else.

nitinkumar · 05-16-2011, 08:17 AM

The contigs are of the rhizobium strains and blast report shows the position where i m getting this type of results have the neighboring nucleotides exactly the same as with query. So I m pretty sure that these are sequencing errors...

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05-11-2011, 05:17 PM	#1
nitinkumar Member Location: UK Join Date: Feb 2011 Posts: 11	blast results I want to edit a blast file in such way that if the query sequence has a gap, that should also comes in the reference sequence like if blast output shows: query: aa-gcaa \|\| \|\|\|\| reference: aatgcaa and I want to remove the t from reference and place a gap... query: aa-gcaa \|\| \|\|\|\| reference: aa-gcaa

05-12-2011, 04:19 AM	#2
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Why? Do you know any programming languages such as Perl, Python, Ruby, Java, etc? If so have a look at BioPerl, Biopython, BioRuby, BioJava etc for libraries to work with BLAST files.

05-12-2011, 09:15 AM	#3
nitinkumar Member Location: UK Join Date: Feb 2011 Posts: 11	Yes I have tried bioperl. but I am not able to do that. I can extract the fasta sequences from these files only..

05-15-2011, 08:38 PM	#4
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	Why not use regexps for, say, finding gap-containing piece of query sequence (20 bp or so) in reference and then removing whatever you want from it?

05-16-2011, 12:21 AM	#5
tomc Member Location: Oregon Join Date: Feb 2011 Posts: 29	you want to copy your query over your reference...? If so, why not just pull you query sequence and use those, they already have the gaps you seem to be looking for. But it does sound odd, maybe a better explanation of why would help.

05-16-2011, 01:43 AM	#6
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	Just taking a query won't work, because it can have different nucleotides (but not gaps) at some sites. After some thinking I see that you don't need any regexps, all you need is like { reference[i]='-' if query[i]='-'; } for each position in sequences. Hope you can grab some sequences, dude. But yes, I'd like to know why he would want to do something like this.

05-16-2011, 04:28 AM	#7
nitinkumar Member Location: UK Join Date: Feb 2011 Posts: 11	Thanks for the reply and I am getting these results because of 454 sequencing errors, the query sequence is the gene of rhizobium bacteria and the subject is the sequence from matching contigs. I want to remove these sequencing errors in contigs. So that I can make the phylogeny of the contigs.

05-16-2011, 05:17 AM	#8
A_Morozov Member Location: Russia, Irkutsk Join Date: Feb 2011 Posts: 40	But so you lose actual indels that could happen between these two species, don't you? I think that first you should make sure that this particular nucleotide is indeed an error. Maybe, it is of quality much less than of other nearby nucleotides, or it is at long repeat like aaaaaaaaa or something else.

05-16-2011, 08:17 AM	#9
nitinkumar Member Location: UK Join Date: Feb 2011 Posts: 11	The contigs are of the rhizobium strains and blast report shows the position where i m getting this type of results have the neighboring nucleotides exactly the same as with query. So I m pretty sure that these are sequencing errors...