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Below are the two files I am working with:

$ cat mys.pep
>00001 16 324  len=309
LDRFYTKKVIMYKQQYFISGKVQGVGFRFFTEQIANNMKLKGFVKNLNDGRVEIVAFFNT
KEQMKKFEKLLNGNKYSNIKNIEKIVLDENYPFQFNDFKIYY*
>00002 751 308  len=398
YKLYNILLIKYFLIFPKYIDNA*I*KNKNYFKTFLLDRFYTKKVIMYKQQYFISGKVQGV
GFRFFTEQIANNMKLKGFVKNLNDGRVEIVAFFNTKEQMKKFEKLLNGNKYSNIKNIEKI

$cat mys.nuc
>00001  16 324  len=309
TTGGATAGATTTTATACAAAGAAGGTAATAATGTATAAACAACAATATTTTATTTCTGGC
AAGGTGCAAGGTGTTGGTTTTAGATTTTTCACAGAGCAAATAGCAAATAATATGAAACTA
AAAGGATTTGTAAAAAATCTCAACGATGGAAGGGTAGAAATTGTAGCTTTCTTTAATACT
AAAGAACAAATGAAAAAATTTGAAAAATTATTAAATGGGAATAAGTATTCAAACATTAAA
AACATTGAAAAAATAGTTTTAGATGAAAATTATCCTTTTCAATTTAATGATTTTAAAATT
TATTATTAG
>00002  751 308  len=398
TACAAATTATATAATATCTTATTAATAAAATATTTCCTAATATTTCCCAAATATATTGAT
AATGCCTGAATTTAAAAAAACAAAAACTATTTTAAAACTTTTCTATTGGATAGATTTTAT
ACAAAGAAGGTAATAATGTATAAACAACAATATTTTATTTCTGGCAAGGTGCAAGGTGTT
GGTTTTAGATTTTTCACAGAGCAAATAGCAAATAATATGAAACTAAAAGGATTTGTAAAA
AATCTCAACGATGGAAGGGTAGAAATTGTAGCTTTCTTTAATACTAAAGAACAAATGAAA
AAATTTGAAAAATTATTAAATGGGAATAAGTATTCAAACATTAAAAACATTGAAAAAATA
GTTTTAGATGAAAATTATCCTTTTCAATTTAATGATTT

What I have done so far is try to run:

$ bioseq -B mys.nuc

and get:

00001
00002

Ultimately I am mean to extract the ORF sequence and save as mys.nuc2 and then translate mys.nuc2 with bioseq -t1 where that file should NOT contain any internal stop codons.

I do not understand why I get:

00001
00002

Or what I am meant to do with it, if that indeed is the correct output.

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  • $\begingroup$ Can you run, which bioseq and whereis bioseq? Also could you add the head bioseq to be sure? How confident are you with writing your own script to find ORF, or download and install (if you can) new tools to do it for you? $\endgroup$
    – llrs
    Feb 14 '18 at 12:26

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