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Old 03-25-2013, 02:34 PM   #1
manojdarolia
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Default 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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Old 03-31-2013, 08:31 AM   #2
Gig77
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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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Old 04-04-2013, 04:33 AM   #3
syfo
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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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