Question: Alternative of ORFFinder for multiple nucleotide sequences
0
gravatar for waqaskhokhar999
6 months ago by
waqaskhokhar99980 wrote:

I have a file that contains multiple sequences in Fasta format. I am interested to translate them and want only protein sequences for the longest ORF. I can do this using ORFFinder but I have to process each sequence individually as it doesn't support multiple sequences. Is there any alternative of ORFFinder that support multiple sequences.?

Sample input:

>BnaA02g12810D

ATGGCTTCCGTTATGCTCTCTTCCGCTACAATGGCCTCTTCTCCGGCTCATGCCACAATGGTCGCACCATTCATCGGACTTAAGTCCTCTGCTGCTTTCCCAGTGACATGTAAGGCCAACACCAAAGTTACTTCCATCACAAGCAACGGCGGAAGAGTTAACTGCATGAAGGTGTGGCCTCCAGTTGGCAAGAAGAAGTTTGAGACTCTCTCTTACCTTCCTGACCTTACCGATGTCGAAATAGCCAAGGAAGTTGACTACCTTATCCGCAACAAGTGGACTCCATGTATTGAATTCGAGTTGGAGCACGGTTTTGTATACCGTGAGCATGGAAACATCCCTGGATACTATGATGGACGATACTGGACAATGTGGAAGCTTCCTTTGTTCGGATGTACTGACTCAGCTCAGGTGTTGAAGGAAGTGCAAGAATGCAAAAAGGAGTACCCCAACGCCTTCATTAGGATCATCGGATTCGACAACAATCGTCAAGCCCAGTGCATCAGTTTCATCGCCTACAAGCCACCAAGCTTCACTAATGCTTAATTACACAGCTTCATTGCTTTGTGTAAACAACAAAACTTTATCCTTCCCTGCCTTTGATTTATCATCTTTTTATATATTTTATCTTTTGTTGTAATTTCCGGATTTAATCTTTGTTTTCCGGGTTGCAAGATATTTTCTTTTGGGTCCTCAAATGTCCTAAAAAATAAATATGTAATGTTATAAAAATATATTATTTTGAATTTTG

>BnaA02g12810D_S31

ATGGCTTCCGTTATGCTCTCTTCCGCTACAATGGCCTCTTCTCCGGCTCATGCCACAATGGTCGCACCATTCATCGGACTTAAGTCCTCTGCTGCTTTCCCAGTGACATGTAAGGCCAACACCAAAGTTACTTCCATCACAAGCAACGGCGGAAGAGTTAACTGCATGAAGGTGTGGCCTCCAGTTGGCAAGAAGAAGTTTGAGACTCTCTCTTACCTTCCTGACCTTACCGATGTCGAAATAGCCAAGGAAGTTGACTACCTTATCCGCAACAAGTGGACTCCATGTATTGAATTCGAGTTGGAGCACGGTTTTGTATACCGTGAGCATGGAAACATCCCTGGATACTATGATGGACGATACTGGACAATGTGGAAGCTTCCTTTGTTCGGATGTACTGACTCAGCTCAGGTGTTGAAGGAAGTGCAAGAATGCAAAAAGGAGTACCCCAACGCCTTCATTAGGATCATCGGATTCGACAACAATCGTCAAGCCCAGTGCATCAGTTTCATCGCCTACAAGCCACCAAGCTTCACTAATGCTTAATTACACAGCTTCATTGCTTTGTGTAAACAACAAAACTTTATCCTTCCCTG

Desired output:

>BnaA02g12810D
MASVMLSSATMASSPAHATMVAPFIGLKSSAAFPVTCKANTKVTSITSNGGRVNCMKVWPPVGKKKFETLSYLPDLTDVEIAKEVDYLIRNKWTPCIEFELEHGFVYREHGNIPGYYDGRYWTMWKLPLFGCTDSAQVLKEVQECKKEYPNAFIRIIGFDNNRQAQCISFIAYKPPSFTNA

>BnaA02g12810D_S31
MASVMLSSATMASSPAHATMVAPFIGLKSSAAFPVTCKANTKVTSITSNGGRVNCMKVWPPVGKKKFETLSYLPDLTDVEIAKEVDYLIRNKWTPCIEFELEHGFVYREHGNIPGYYDGRYWTMWKLPLFGCTDSAQVLKEVQECKKEYPNAFIRIIGFDNNRQAQCISFIAYKPPSFTNA
rna-seq translation orf • 159 views
ADD COMMENTlink modified 6 months ago by genomax89k • written 6 months ago by waqaskhokhar99980
2
gravatar for genomax
6 months ago by
genomax89k
United States
genomax89k wrote:

You could download linux version available here and run that in a loop for your sequences. There is also EMBOSS getorf program that may be of interest.

ADD COMMENTlink written 6 months ago by genomax89k

Many thanks, Can you please suggest me how I can design loop for it?

ADD REPLYlink written 6 months ago by waqaskhokhar99980
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