Hello,
The tool is called awk.
There is also another tool called Perl, but I won't recommend it.
Regards,
F.
On 05/08/2012 04:02 PM, K Singh wrote:
Dear All
I was looking for a script or an informatics tool enabling me to
change the sequence from FASTA format to something like following:
FAS
More seriously, there is the babel command from Open Babel
in case the second format you show has a known name.
On 05/08/2012 04:46 PM, Francois Berenger wrote:
Hello,
The tool is called awk.
There is also another tool called Perl, but I won't recommend it.
Regards,
F.
On 05/08/2012 04:02 PM,
Surely a sequence analysis tools are the easiest way to do it.
I'd recommend EMBOSS (open source and runs nicely on most platforms - the
"ccp4" of sequence analysis for me at least)
http://emboss.sourceforge.net/
Seqret (SEQuence RETurn) program:
seqret -out test.seq -osformat gcg test.fasta
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Kris,
except for formatting, something like this:
sed -e "s/\(.\)\(.\)/ \1 \2\n/g" test.fasta | awk '{count =
(10*LN +1); print count, $0; ++LN}'
(all on one line)
should do the job.
Cheers, Tim
On 05/08/12 09:02, K Singh wrote:
> D
AIL.AC.UK
>Sent: Tuesday, May 8, 2012 12:32 PM
>Subject: [ccp4bb] sequence format conversion
>
>Dear All
>I was looking for a script or an informatics tool enabling me to
>change the sequence from FASTA format to something like following:
>
>>FASTA FORMAT
>abcdefghijklm
On Tue, 2012-05-08 at 09:22 +0100, Marko Hyvonen wrote:
> PS. fasta format needs ">" as a first line with (optional) description in
> the input file. And not sure what amino acids "b" and "j" would get
> converted to :-)
A good tool should leave "b" as is: it is ASX (the standard ambiguity
code
A good tool should leave "b" as is: it is ASX (the standard ambiguity
code for ASP or ASN). "j", "o" and "u" are a different matter :-)
http://www.uniprot.org/manual/non_std
"Selenocyteine [sic!] and pyrrolysine are represented in the sequence using
the one-letter codes U for selenocysteine an
K-
One bioinformatics tool that converts nucleitude sequence formats across many
such formats is Biology Workbench, out of UCSD
Dexter Kennedy, MD
Thumbed from my iPhone
On May 8, 2012, at 12:02 AM, K Singh wrote:
> Dear All
> I was looking for a script or an informatics tool enabling me to
>
