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Old 11-13-2009, 01:20 AM   #1
Junior Member
Location: Brussels

Join Date: Nov 2009
Posts: 3
Default Viewers for Blast and Blat alignments

Hello everyone,

I am new in the field of bioinformatics and I am currently looking for a good alignment viewer. I have run several alignments using blast and blat software and would like to view the resulting alignments (RNA-seq).

I made some researches and found several viewers including SAMtools, MapView, MAQ viewer, GAP5, Consed or even the ShortRead package from Bioconductor, but none of them seems to be able to read output from Blast of Blat (.psl).

Since SAMtools can handle gapped alignments, I tried to use the third party convertors that come with it (such as psl2sam) but it does not seem to work correctly. The only official convertor that comes with SAMtools takes MAQ files as input, which I do not have. Other viewers such as MapView or GAP5 also rely on other input formats such as MAQ or ELAND.

So my question is simple. Do you know if there are viewers that can handle blast and blat alignments directly or indirectly (using approved converters), or do you think it would be faster to develop my own viewer to handle this particular problem of input format ?

dgacquer is offline   Reply With Quote
Old 11-16-2009, 02:55 AM   #2
Location: Netherlands

Join Date: Sep 2009
Posts: 18

It depends on what you exactly want to view!
If you want to view annotations...have a look at the Artemis viewer from Sanger. That will do the job.
If you want to use BLAST/BLAT for bigblast genome comparisons you might want to look in alternative methods but Artemis can read those as well if I remember correctly. For this purpose I wrote a wrapper around mummer and port all my data to Artemis viewer and Artemis comparsion tool (ACT).
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Old 11-16-2009, 07:00 AM   #3
Location: Maryland

Join Date: May 2009
Posts: 25

See the answer in the following post describing the use of Galaxy.
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Old 12-23-2009, 09:07 AM   #4
(Jeremy Leipzig)
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116

there is nothing wrong with your approach (BLAST->sam->viewer) but samtools is really meant for handling millions of short read alignments.

If you have a few hundred you might just want to convert directly to gff3 and view in gbrowse or jbrowse


Jeremy Leipzig
Bioinformatics Programmer
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Old 01-09-2010, 08:33 PM   #5
Location: wenzhou.zhejiang.china

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Posts: 23

try this
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