mothods for analyzing exons area

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9.1 years ago

akbioinfo14 • 0

i want to know is there any tool to seperate only functional area i.e exons from whole DNA sequence?

sequencing • 1.5k views

ADD COMMENT • link updated 23 months ago by Ram 43k • written 9.1 years ago by akbioinfo14 • 0

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Whole DNA sequence of what? NGS? Genbank? How To Ask Good Questions On Technical And Scientific Forums

ADD REPLY • link updated 23 months ago by Ram 43k • written 9.1 years ago by Pierre Lindenbaum 161k

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whole DNA sequence of any organism

ADD REPLY • link updated 23 months ago by Ram 43k • written 9.1 years ago by akbioinfo14 • 0

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So you want to extract exonic sequences from the reference fasta sequence?

ADD REPLY • link 9.1 years ago by Ashutosh Pandey 12k

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s exactly !!!!

ADD REPLY • link 9.1 years ago by akbioinfo14 • 0

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Go to biomart and you can download the gtf files containing the location of the exons. You can then easily extract it from the fasta files

ADD REPLY • link updated 23 months ago by Ram 43k • written 9.1 years ago by Sam ★ 4.7k

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You can download bed file for these exons using UCSC Table browser. The bed file will have chromosome name, start and end location for that exon. You can then use samtools faidx or Picard's ExtractSequences program to extract them.

ADD REPLY • link updated 23 months ago by Ram 43k • written 9.1 years ago by Ashutosh Pandey 12k

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