Extracting protein sequences

Question

[h.l.wong]

Hi all,

I have got some bins on hand, after checking the completeness with checkM, I uploaded the .faa amino acid sequences to GhostKoala for functional annotation.

I would like to pull out specific dsrAB sequences and then build a tree with MEGA.

I opened the file from GhostKoala and the contig containing the dsrAB were located at: >contig_121_354180_length_26085_multi_13_in_2_out_2_7 However, I cannot find that contig in the .faa amino acid files.

What programs do you recommend that can pull out targeted amino acid sequences? And is MEGA alone enough to build a maximum likelihood tree or do I need to use more programs?

Cheers and many thanks

Alan