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Old 07-03-2013, 05:39 AM   #1
atape
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Default Software for aligning cDNA onto reference genomic sequences to retrieve INTRONS

Hi,

which software would you recommend for the task? I need to retrieve introns from genomic sequences by aligning cDNAs on to them.

Thank you

Last edited by atape; 07-03-2013 at 05:47 AM.
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Old 07-03-2013, 06:11 AM   #2
GenoMax
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You should be able to use blat (http://genome.ucsc.edu/FAQ/FAQblat.html) for that purpose. In fact the web version of blat will display exons/introns with distinct color.
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Old 07-03-2013, 09:29 AM   #3
lh3
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Blat or GMAP or exonerate.
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Old 07-05-2013, 03:11 AM   #4
atape
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Thanks guys and gals

Exonerate is working out nicely, but will try all the algorithms that have been listed, just to see which gives the most favourable results.

One more thing though, what would be the easiest (most structured) way to view/edit the sequences I get?

Viewing and editing them in something like MEGA is not the best option I feel.
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Old 07-05-2013, 03:41 AM   #5
JackieBadger
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As far as I am aware BLAT doesn't identify splice sites....?
Your thread title says "DNA onto genomic.."...but then yo go on to say "cDNA".
cDNA needs to have special considerations when aligning to genomic regions.

Try TopHat or Newbler
You can view easily with Tablet.
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Old 07-05-2013, 04:02 AM   #6
kmcarr
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Quote:
Originally Posted by JackieBadger View Post
As far as I am aware BLAT doesn't identify splice sites....?
Your thread title says "DNA onto genomic.."...but then yo go on to say "cDNA".
cDNA needs to have special considerations when aligning to genomic regions.

Try TopHat or Newbler
You can view easily with Tablet.
BLAT performs quite well with spliced alignments (ESTs, mRNA, cDNA) to genomic DNA. These types of alignments were part of its original design intent.
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Old 07-05-2013, 04:45 AM   #7
JackieBadger
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Thats good to know. However BLAT may not perform very well in trans-species alignments and only return alignments if the sequence identity is > 95% or so.
Just something to consider
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Old 07-05-2013, 08:51 AM   #8
kmcarr
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Quote:
Originally Posted by JackieBadger View Post
Thats good to know. However BLAT may not perform very well in trans-species alignments and only return alignments if the sequence identity is > 95% or so.
Just something to consider
Not true. The first two sentences of Jim Kent's abstract for his BLAT paper
Quote:
Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.
As you see he specifically designed BLAT with cross-species alignments in mind.
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Old 07-05-2013, 09:34 AM   #9
JackieBadger
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I stand corrected
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