convert DNA FASTA file to RNA FASTA file

Question

[xiaoleiusc]

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

[Ram]

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"?

[xiaoleiusc]

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

Answer 1

[Mensur Dlakic]

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.

[xiaoleiusc]

Hi, Mensur,

Thank you very much for introducing the esl-reformat.

Xiao

Answer 2

[JC]

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

[xiaoleiusc]

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

Xiao