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Old 09-08-2014, 07:34 AM   #1
huma Asif
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Default MUltifasta file

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

Last edited by huma Asif; 09-08-2014 at 10:13 AM.
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Old 09-08-2014, 07:38 AM   #2
GenoMax
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Do you want to know how to do the renaming or is this just an informational post?
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Old 09-08-2014, 08:10 AM   #3
huma Asif
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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

Last edited by huma Asif; 09-08-2014 at 10:28 AM.
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Old 09-08-2014, 10:52 AM   #4
GenoMax
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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?
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Old 09-08-2014, 11:09 AM   #5
HMorrison
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Quote:
Originally Posted by GenoMax View Post
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.
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Old 09-08-2014, 11:12 AM   #6
huma Asif
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GenoMax
yes
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Old 09-08-2014, 11:19 AM   #7
GenoMax
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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?
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Old 09-08-2014, 11:24 AM   #8
huma Asif
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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
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