amino acid support

[jianshu93]

Hello COBS team,

Any possibilities to also support amino acid sequences (20 alphabets instead of 4 for DNA). I found this to be extremely useful for genome query/search.

Thanks,

Jianshu

[iqbal-lab]

Should already support amino acid sequences in the sense that it indexes free text. Pass in a .txt file of amino acids and see how you go?

[jianshu93]

Thanks for quick response. I saw that fasta file in test folder is amino acid sequence. for example sample6.fasta. I will try now.

Thanks

Jianshu

[iqbal-lab]

Note that by default it tries to canonicalize kmers (taking kmer and reverse complement and choosing smaller). See this text from the README:

With the flag --no-canonicalize any letters or text can be indexed.