Removing recombination/nucleotide sequences, from fasta files

Question

[natasha]

Hi

I have used clonalframeML to find areas of recombination within my isolates, but I am unsure of how to remove these areas of recombination from each of my isolates sequence fasta. Can anyone help?

I can use cutSeq to extract the nucleotide sequences of recombination and am able to save these in separate fasta files. For example the output of cutSeq provides me with;

>>C9-2007 255226..255835
AAGAATGGAATACGCCGCCAATCAACTGATGTTTGATACCGGCTCATCGGTGCTAGACATTGCTAACAAG
TGCGGCTTTAACTC...
>C9-2007 2828176..2839383
CAGGAAATATTAGCGATGATTTTTTCGCAAAAATTAAAAACATCAATTAATCAAAAGGTTAAAAATAAGA
AGAAGACATT...
>C9-2007 2955993..2969778
CCATAGATAACCTATTACCGAA-TAAATTTGCGTTAAAACTGCCGCAACTATGACACTAACCCTAGGCGA
CTTCAAGAC...
>C9-2007 3554396..3559290
TCTTTATACAGTAAAGATGAGCGGGAATATTTTTATCTAACAGGTTATTTTTTGTGATGAGGTGGGAAAA
ATGAGTCGAA...

However how do I remove these sequences from the original fasta sequence? CutSeq only copies and pastes the recombination, but does not remove it.

Answer 1

[Pierre Lindenbaum]

extract the region from the fasta header to create a BED file and then use: bedtools maskfasta or bedtools getfasta

[natasha]

Thank you so much