Software For Aligning Cdna Onto Reference Genomic Sequences To Retrieve Introns

Question

[atapee]

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

[fridhackery]

If your organism is well annotated, you can skip the alignment part. Retrieve the exon coordinates, then adjust that table to give you the gaps between the exons, then retrieve those sequences.

[atapee]

Thank you,

I've been doing that, the main problem is that I don't have a good way od viewing/editing the sequences I get.

Got any advice on an editor or other way i could optimise this?

[fridhackery]

Bedtools. Make a bed file of all desired intron positions, then use fastaFromBed to extract the sequences from your reference genome

[Pierre Lindenbaum]

cross posted on seqanswers of http://seqanswers.com/forums/showthread.php?p=109615

Answer 1

[Malcolm.Cook]

exonerate

Answer 2

[Hamish]

This is a typical problem when mapping cDNA or EST sequences to genomic genes, and so there are quite a few options, for example:

• EMBOSS est2genome: http://emboss.open-bio.org/rel/rel6/apps/est2genome.html
• sim4: http://globin.bx.psu.edu/html/docs/sim4.html
• SSAHA2 and ssahaEST
• FASTA suite GLSEARCH: a global/local pairwise alignment search tool

Sequence assembly suites, for example Staden or CAP3, commonly support alignment of fragment sequences against a reference contig/genome and thus may also be used for this task. See the Wikipedia pages "List of sequence alignment software" and "Sequence assembly" for a range of alignment and sequence assembly tools including a selection of programs designed for this task.

Answer 3

[Pierre Lindenbaum]

BLAT