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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

cdna intron reference alignment database software est
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by atapee • atapee

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.

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written by fridhackery • fridhackery

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?

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written by atapee • atapee

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

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written by fridhackery • fridhackery

3 answers

exonerate

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written by Malcolm.Cook Malcolm.Cook

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

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.

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written by Hamish Hamish

BLAT

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written by Pierre Lindenbaum Pierre Lindenbaum

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