Alternative of ORFFinder for multiple nucleotide sequences

Question

[waqaskhokhar999]

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

Answer 1

[GenoMax]

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.

[waqaskhokhar999]

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