MUltifasta file

[huma Asif]

hi every one,

what i need to do is i need multiple sequence alignment file

i converted the vcf file to consensus fasta and "cat" all these consensus sequence into multifasta.



in my cat file seq are >1......>10000 for a.fasta and >1......>10000 for b.fasta when i use clustal w it gives error that sequence have same header THAT MAKES SENSE so what i am planning to do is to convert >1..>2...>3.>10000 to >1

and >1..>2..>3..>10000 for b.fasta to >2 and same for for all my 5 samples
i have to use this file for multiple alignment
Regards

[GenoMax]

Do you want to know how to do the renaming or is this just an informational post?

[huma Asif]

how i can convert
>1...>2....>3...>10000 to >1

and
>1..>2..>3....>10000 for b.fasta to >2 and
same for for all my 5 samples
i have to use this file for multiple alignment

[GenoMax]

You want to convert every fasta ID header from multiple fasta sequences in file "a" to >1 and from file "b" to >2, is that correct?

[HMorrison]

You want to convert every fasta ID header from multiple fasta sequences in file "a" to >1 and from file "b" to >2, is that correct?

That won't give them unique deflines, which I think is what he/she is after for input to clustalw. I still can't tell what the problem is, though.

[huma Asif]

GenoMax
yes

[GenoMax]

If you rename all of them as >1 or >2 for a sample the sequences ID's would no longer be unique.

What kind of MSA are you trying to do?

[huma Asif]

i want all the genes e.g in sample 1 to be concatenated as >1 likewise for my all samples
my thought is as all genes in all files are in same order so when i have multifasta as >1, >2, >3,>4,>5
i will take that multifasta to do alignment around these interval