FASTA(1) User Commands FASTA(1)NAME
famap - prepare Fasta sequence database for re-PCR searches
SYNOPSIS
famap [-hV] -b mmapped-file [-t cvt] [fafile ...]
famap [-hV] -d mmapped-file [ord ...]
famap [-hV] -l mmapped-file [ord ...]
DESCRIPTION
The program famap is part of the e-PCR suite and is used to build mmapped-file from FASTA files for reverse e-PCR searches
OPTIONS
where cvt (conversion table) is one of:
off - as is (default)
n - nucleotide [acgtnACGTN] allowed,
N - nucleotide uppercase allowed [ACGTN]
nx - nucleotide with ambiguity codes allowed
NX - nucleotide with ambiguity codes uppercase
EXAMPLE
famap -tN -b genome.famap org/chr_*.fa
fahash -b genome.hash -w 12 -f3 ${PWD}/genome.famap
re-PCR -s genome.hash -n1 -g1 ACTATTGATGATGA AGGTAGATGTTTTT 120-200
See famap(1) and re-pcr(1)SEE ALSO
/usr/share/doc/ncbi-epcr/README.txt
bioperl(1), e-pcr(1), famap(1) and re-pcr(1)AUTHORS
This manual page was written by Andreas Tille <tille@debian.org> for the Debian system (but may be used by others). Permission is granted
to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by
the Free Software Foundation.
On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL.
Fasta converter for e-PCR version 2.3.9 April 2008 FASTA(1)
Check Out this Related Man Page
Ingests(1) General Commands Manual Ingests(1)NAME
ingests - Build an auxiliary file for multicat
SYNOPSIS
ingests -p <PCR PID> [-m <payload size>]>] <input ts>
DESCRIPTION
Ingests is a companion application designed to manipulate TS files. It reads the PCR values of the file, and builds the auxiliary file that
is necessary for multicat. The combination of ingests and multicat makes a simple and efficient TS file streamer.
OPTIONS -m <payloadsize> Size of the payload
-h Show summary of options
-m <payloadsize>
Size of the payload
-p <PCR PID>
PCR PID to use
SEE ALSO aggregartp(1). desaggregartp(1). multicat(1), offsets(1).
Read the README file for more information about the configuration of ingests.
AUTHOR
ingests was written by Christophe Massiot.
LICENCE
This program is free software; you can redistribute it and/or modify it under the terms of version 2 of the GNU General Public License as
published by the Free Software Foundation.
This manual page was written by Remi Duraffort <ivoire at videolan dot org>, for the Debian project (and may be used by others).
Multicat 1.0 August 23, 2010 Ingests(1)
For example, if I have the file whose content are:
>HWI-EAS382_30FC7AAXX:7:1:927:1368
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
>HWI-EAS382_30FC7AAXX:7:1:924:1373
ACGAACTTTAAAGCACCTCTTGGCTCGTATGCCGTC
I want my output calculate the total of nucleotide. So my output should look like this:... (2 Replies)
Hi all,
I am very new in programming.
Can anyone please help me in the matter below?
I have one raw file like:
gi|77|ref|NC_002971.3| Coxiella burnetii RSA 493, complete genome 6371 ATCGTGGTTGTGGTTCAT 5032 P 2 12
gi|71|ref|NC_005773.3| Pseudomonas syringae pv.... (4 Replies)
I would like to extract the sequences larger than 10 bases but shorter than 18 along with the identifier from a FASTA file that looks like this:
> Seq I
ACGACTAGACGATAGACGATAGA
> Seq 2
ACGATGACGTAGCAGT
> Seq 3
ACGATACGAT
I know I can extract the IDs alone with the following code
grep... (3 Replies)
I really need some help with this task. I have a bunch of FASTA files with hundreds of DNA sequences that look like this:
>SeqID1
AACCATGACAGAGGAGATGTGAACAGATAGAGGGATGACAGATGACAGATAGACCCAGAC
TGACAGGTTCAAAGGCTGCAGTGCAGTGACGTGACGATTT
>Sequence 22... (13 Replies)
I have a FASTA file with thousands of sequences that looks something like this:
I need to modfy the header in such way that everything after the dot is remove. Thus, I will end up with something like this:
Thanks (1 Reply)