mothods for analyzing exons area

0

Entering edit mode

9.7 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 • 1.6k views

ADD COMMENT • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by akbioinfo14 • 0

0

Entering edit mode

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

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by Pierre Lindenbaum 164k

0

Entering edit mode

whole DNA sequence of any organism

ADD REPLY • link updated 2.5 years ago by Ram 44k • written 9.7 years ago by akbioinfo14 • 0

0

Entering edit mode

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

ADD REPLY • link 9.7 years ago by Ashutosh Pandey 12k

0

Entering edit mode

s exactly !!!!

ADD REPLY • link 9.7 years ago by akbioinfo14 • 0

0

Entering edit mode

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 2.5 years ago by Ram 44k • written 9.7 years ago by Sam ★ 4.8k

0

Entering edit mode

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 2.5 years ago by Ram 44k • written 9.7 years ago by Ashutosh Pandey 12k

Login before adding your answer.