I am working on FIV and have sequenced each gene individually and retrieved multiple complete genomes and individual genes from Genbank. I am trying to align all the different genes to the complete genome. I need a program that can align each individual sequence to one reference sequence. I have tried MEGA but from what I understand the pairwise alignment compares 2 subsequent sequences in the list and tries to align them then the next pair and so forth (this won't work as I don't want to align different genes), while the multiple sequence alignment tries to align each sequence to all the other sequences (this also won't work for the same reason). Is there a setting in MEGA that will allow me to set a reference sequences to which it must compare all other sequences to or another program that will allow me to do this.
The only other option I can think of is to compare each sequence individually to the reference sequence and that will be a nightmare as I have 4289 sequences. Please if you have any suggestions let me know. Thank you.
Hi,
you can use MUSCLE. It allows you to align two alignments with each other (known as profile-profile alignment),
For single sequence in the profile:-
muscle -profile -in1 first.fasta -in2 second..fasta -out combined_result.fasta
this aligns the alignments in the two files first.fasta and second.fasta to each other and writes them to combined_result.fasta
You can also do the same profiles thing with Mafft.
http://mafft.cbrc.jp/alignment/software/addsequences.html
https://mafft.cbrc.jp/alignment/software/
with ClustalW2:-
clustalw2 -profile1=data.fa -sequences -profile2=first.fa
assuming one seq is first.fa and the prealigned others are in data.fa
you can also look AVID
Bray, N., Dubchak, I. and Pachter, L. (2003) AVID: A Global Alignment Program. Genome Res., 13:97
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