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03-25-2013, 02:34 PM
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#1 |
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Junior Member
Location: USA Join Date: Sep 2010
Posts: 2
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hot to calculate mean and median exon/intron sizes
hey there
I have cDNA and their genomic sequences in fasta files separately. now i want to calculate mean and median exon/intron lenght, sizes of UTR. how can i do that. any suggestions??? Thanks |
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03-31-2013, 08:31 AM
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#2 |
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Member
Location: Canada Join Date: Jun 2012
Posts: 17
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If you only have cDNA and genomic sequences (without gene models), you will have to align your cDNA sequences first against the genomic sequences to get exon coordinates (using e.g. BLAT). From these coordinates you should be able to derive exon/intron lengths.
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04-04-2013, 04:33 AM
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#3 |
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Just a member
Location: Southern EU Join Date: Nov 2012
Posts: 103
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Exactly. And if you can assume that your cDNAs are "full-length" you can run an ORF detector on them to estimate CDS & UTR size distribution.
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