How to add specific bases at the beginning and ending of all the fasta sequences?
Hi,
I have to add 7 bases of specific nucleotide at the beginning and ending of all the fasta sequences of a file. For example, I have a multi fasta file namely test.fasta as given below
I need to add the following bases CTGATAGTA at the beginning and ending of every fasta sequences respectively.
I have tried the following command line to add bases at the end of fasta file, but it is not serving my purpose,
. For adding bases at the beginning I do not have any idea, However, I tried the following command
, but its adding bases at the fasta header.
Please help me to do the same.
Thank you.
I have got an Perl array like:
@array = (1,2,3,4,5,6,1,2,3,4,1,2,1,2,3,4,5,6,7,8,9...............)
This numeric sequence will be always sequentially increasing, unless it encounters, The beginning of the new sequentially increasing numeric sequence.
SO in this array we get sequentially... (5 Replies)
Hi, I have multiple large files which consist of the below format:
I am trying to write an awk or sed script to remove all occurrences of the 00 record except the first and remove all of the 80 records except the last one.
Any help would be greatly appreciated. (10 Replies)
Hi,
I am having a file of dna sequences in fasta format which look like this:
>admin_1_45
atatagcaga
>admin_1_46
atatagcagaatatatat
with many such thousands of sequences in a single file. I want to the replace the accession Id "admin_1_45" similarly in following sequences to... (5 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
I have a fasta file as follows
>sp|O15090|FABP4_HUMAN Fatty acid-binding protein, adipocyte OS=Homo sapiens GN=FABP4 PE=1 SV=3
MCDAFVGTWKLVSSENFDDYMKEVGVGFATRKVAGMAKPNMIISVNGDVITIKSESTFKN
TEISFILGQEFDEVTADDRKVKSTITLDGGVLVHVQKWDGKSTTIKRKREDDKLVVECVM
KGVTSTRVYERA
>sp|L18484|AP2A2_RAT AP-2... (3 Replies)
Hi
How can I extract sequences from a fasta file with respect a certain criteria? The beginning of my file (containing in total more than 1000 sequences) looks like this:
>H8V34IS02I59VP
SDACNDLTIALLQIAREVRVCNPTFSFRWHPQVKDEVMRECFDCIRQGLG
YPSMRNDPILIANCMNWHGHPLEEARQWVHQACMSPCPSTKHGFQPFRMA... (6 Replies)
Hi,
I have a fasta file with multiple sequences. How can i get only unique sequences from the file.
For example
my_file.fasta
>seq1
TCTCAAAGAAAGCTGTGCTGCATACTGTACAAAACTTTGTCTGGAGAGATGGAGAATCTCATTGACTTTACAGGTGTGGACGGTCTTCAGAGATGGCTCAAGCTAACATTCCCTGACACACCTATAGGGAAAGAGCTAAC
>seq2... (3 Replies)
I could calculate the length of entire fasta sequences by following command,
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' unique.fasta
But, I need to calculate the length of a particular fasta sequence specified/listed in another txt file. The results to to be... (14 Replies)
I have a fasta file as follows
>sp|Q8WWQ8|STAB2_HUMAN Stabilin-2 OS=Homo sapiens OX=9606 GN=STAB2 PE=1 SV=3
MMLQHLVIFCLGLVVQNFCSPAETTGQARRCDRKSLLTIRTECRSCALNLGVKCPDGYTM
ITSGSVGVRDCRYTFEVRTYSLSLPGCRHICRKDYLQPRCCPGRWGPDCIECPGGAGSPC
NGRGSCAEGMEGNGTCSCQEGFGGTACETCADDNLFGPSCSSVCNCVHGVCNSGLDGDGT... (3 Replies)
I have to mine the following sequence pattern from a large fasta file namely gene.fasta (contains multiple fasta sequences) along with the flanking sequences of 5 bases at starting position and ending position,
AAGCZ-N16-AAGCZ
Z represents A, C or G (Except T)
N16 represents any of the four... (3 Replies)
Discussion started by: dineshkumarsrk
3 Replies
LEARN ABOUT DEBIAN
ampliconnoise
AMPLICONNOISE(1) AmpliconNoise Documentation AMPLICONNOISE(1)NAME
AmpliconNoise - remove noise from high throughput nucleotide sequence data
VERSION
This documentation refers to version 1.22
SYNOPSIS
See /usr/share/doc/ampliconnoise/Doc.pdf.gz for details of how to run.
DESCRIPTION
The following tools are included. Most of them have an MPI equivalent, for example SeqNoise has an equivalent SeqNoiseM which can be used
with mpirun.
FastaUnique - dereplicates fasta file
-in string input file name
Options:
FCluster
-in string distance input file name
-out string output file stub
Options:
-r resolution
-a average linkage
-w use weights
-i read identifiers
-s scale dist.
NDist - pairwise Needleman-Wunsch sequence distance matrix from a fasta file
-in string fata file name
Options:
-i output identifiers
Perseus - slays monsters
-sin string seq file name
Options:
-tin string reference sequence file
-a output alignments
-d use imbalance
-rin string lookup file name
PyroDist - pairwise distance matrix from flowgrams
-in string flow file name
-out stub out file stub
Options:
-ni no index in dat file
-rin string lookup file name
PyroNoise - clusters flowgrams without alignments
-din string flow file name
-out string cluster input file name
-lin string list file
Options:
-v verbose
-c double initial cut-off
-ni no index in dat file
-s double precision
-rin file lookup file name
SeqDist - pairwise distance matrix from a fasta file
-in string fasta file name
Options:
-i output identifiers
-rin string lookup file name
SeqNoise - clusters sequences
-in string sequence file name
-din string distance matrix file name
-out string cluster input file name
-lin string list file
Options:
-min mapping file
-v verbose
-c double initial cut-off
-s double precision
-rin string lookup file name
SplitClusterEven
-din string dat filename
-min string map filename
-tin string tree filename
-s split size
-m min size
AUTHOR
All software by Chris Quince (quince@civil.gla.ac.uk) This manpage by Tim Booth (tbooth@ceh.ac.uk)
LICENCE AND COPYRIGHT
Copyright (c) 2009 (quince@civil.gla.ac.uk). All rights reserved.
Released under the Lesser GPL.
Permission is granted for anyone to copy, use, or modify these programs and documents for purposes of research or education, provided this
copyright notice is retained, and note is made of any changes that have been made.
perl v5.12.4 2011-04-28 AMPLICONNOISE(1)