Question: convert DNA FASTA file to RNA FASTA file
0
gravatar for xiaoleiusc
10 days ago by
xiaoleiusc70
USA/New York/The Rockefeller University
xiaoleiusc70 wrote:

Hi, All,

Is there a tool to convert a DNA FASTA file to an RNA FASTA file? I know there are online servers that could accept DNA sequences and do the conversion, however, it seems that these servers do not accept DNA FASTA files.

Thanks,

Xiao

rna-seq chip-seq sequence • 71 views
ADD COMMENTlink modified 10 days ago by JC12k • written 10 days ago by xiaoleiusc70

There is no such thing as DNA FASTA and RNA FASTA. What operations are referring to here? Is it reverse complement + changing Ts to Us? If so, you'll need to chain those two operations.

Can you show us some online tools that do what you want "but not on files"?

ADD REPLYlink written 10 days ago by Ram32k

Hi, Ram,

Sorry for the confusion. I mean changing T s to U s (not reverse complement). Basically, I have a DNA file in FASTA format, and I would like to change the T s in the DNA to U s.

Thanks. Xiao

ADD REPLYlink written 10 days ago by xiaoleiusc70
1
gravatar for Mensur Dlakic
10 days ago by
Mensur Dlakic9.1k
USA
Mensur Dlakic9.1k wrote:

esl-reformat from the easel package - also gets compiled as part of HMMer - will do all kinds of biological sequence conversions, including what you need.

ADD COMMENTlink written 10 days ago by Mensur Dlakic9.1k

Hi, Mensur,

Thank you very much for introducing the esl-reformat.

Xiao

ADD REPLYlink written 10 days ago by xiaoleiusc70
1
gravatar for JC
10 days ago by
JC12k
Mexico
JC12k wrote:

The servers I am aware can accept DNA/RNA with autodetection, but you can convert it as:

$ cat test.fa
>seq_0
ATGCTTACTGGGTGATC
>seq_1
TTGCCTCACCGNACTGC
>seq_2
ACTGATTCGCCTAATAA
$ perl -pe 'tr/tT/uU/ unless(/>/)' < test.fa
>seq_0
AUGCUUACUGGGUGAUC
>seq_1
UUGCCUCACCGNACUGC
>seq_2
ACUGAUUCGCCUAAUAA
ADD COMMENTlink written 10 days ago by JC12k

Hi, JC, Your Perl script works well! Thanks.

Xiao

ADD REPLYlink written 10 days ago by xiaoleiusc70
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