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Old 05-28-2010, 03:22 AM   #1
Balat
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Default software for aligning ESTs to reference genome

Hi,
I want to know about the programs to align ESTs to reference genome. I have denovo contigs made from Illumina reads. We have a reference genome sequence which is not fully annotated. Is there any progam that I can use to align my contigs (ESTs) to the reference genome?
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Old 05-28-2010, 05:53 AM   #2
dcfargo
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The trans-ABySS 'pipeline' suggests BLAT or Exonerate.

http://www.bioperl.org/wiki/Exonerate
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Old 05-31-2010, 10:53 PM   #3
KevinLam
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as an alternative you may wish to try the method that Matz lab has published.
http://kevin-gattaca.blogspot.com/20...udget-ngs.html

Tools used are
- Blast executables from NCBI, including blast, blastcl3, and blastclust
- Washington University blast (Wu-blast)
- ESTate sequence clustering software
- Perl

They started out with 454 reads assembled as a reference transcriptome to align SOLiD reads to it. Sounds similar to your problem.
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Old 06-28-2010, 06:21 AM   #4
rahul.m.dhodapkar
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Hey,
does anyone know what the default output settings for Exonerate are? Is there an option for outputting alignments in SAM format?

Thanks all.
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Old 07-02-2010, 03:50 PM   #5
lifeng.tian
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A partial list of EST/Genome alignment software I used:
1. BLAT http://genome.ucsc.edu/
2. ssahaEST http://www.sanger.ac.uk/resources/software/ssahaest/
3. Exalin http://blast.wustl.edu/exalin/
4. GMAP http://research-pub.gene.com/gmap/
5. BLAST

Quote:
Originally Posted by Balat View Post
Hi,
I want to know about the programs to align ESTs to reference genome. I have denovo contigs made from Illumina reads. We have a reference genome sequence which is not fully annotated. Is there any progam that I can use to align my contigs (ESTs) to the reference genome?
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