Align genome sequences

Question

[p.rajan]

HI ALL I need to analyze few whole genome sequences of phages . In order for me to do that i need to have the same start point for all these phages. Right now lot of these phages are quite similar but they have different start points hence im not able to to see the mutations. I have done multiple genome alignments using clustal omega but i see a lot of gaps in these phages which i assume is because they are not aligned properly. how to arrange them so that they all have the same start point?

Thanks

Prianka

Answer 1

[shenwei356]

For me, I align the genomes with Mauve and get coordinates from the .backbone file. Then I can reset the start position using my Perl script fasta_reset_start_position_for_circular_genome.pl, which has no extra dependency except for Perl. Just download and run.

For example:

Original seq:  |---------------|-------------------------|
                               |new start
New seq:                       |-------------------------|---------------|

$ cat seq.fa
>seq
actgnACTGN

$ fasta_reset_start_position_for_circular_genome.pl seq.fa 6

$ cat seq.newstart6.fa
>seq (start position move to 6)
ACTGNactgn

Before resetting start position, you may also need to get the reverse complementary sequence with other tools, like seqkit (seqkit seq -r -p seq.fa > seq.rc.fa) or seqtk (seqtk seq -r seq.fa > seq.rc.fa).

Answer 2

[p.rajan]

Hi Thanks for your response. Is there any other way out like using MEGA software to align these at the same start position?

[shenwei356]

Please click buttern ADD COMMENT to response to answers.

Why not MEGA?