Dear Collegues
I have to extract Some pattern from raw text file using perl
The input will be raw text.
Pattern to get - Sequence of Capital Letter Words ( e.g. he is working in Center for Perl Studies. He will come tomorrow...) from thos I have to extract sequences like "Center for Perl... (5 Replies)
Hi,
I have an one-line file consisting of a sequence of 660 letters. I would like to extract 9-letter blocks iteratively:
ASDFGHJKLQWERTYUIOPZXCVBNM
first block: ASDFGHJKL
1nd block: SDFGHJKLQ
What I have so far only gives me the first block, can anyone please explain why?
cat... (7 Replies)
Hi.. I have a seperate chromosome sequences and i wanted to parse some regions of chromosome based on start site and end site.. how can i achieve this?
For Example Chr 1 is in following format
I need regions from 2 - 10 should give me AATTCCAAA
and in a similar way 15- 25 should give... (8 Replies)
Hi
I have an alignment file (.fasta) with ~80 sequences. They look like this-
>JV101.contig00066(+):25302-42404|sequence_index=0|block_index=4|species=JV101|JV101_4_0
GAGGTTAATTATCGATAACGTTTAATTAAAGTGTTTAGGTGTCATAATTT
TAAATGACGATTTCTCATTACCATACACCTAAATTATCATCAATCTGAAT... (2 Replies)
I have fasta files with multiple sequences in each. I need to change the sequence name headers from:
>accD:_59176-60699
ATGGAAAAGTGGAGGATTTATTCGTTTCAGAAGGAGTTCGAACGCA
>atpA_(reverse_strand):_showing_revcomp_of_10525-12048
ATGGTAACCATTCAAGCCGACGAAATTAGTAATCTTATCCGGGAAC... (2 Replies)
I have two files. File1 is shown below.
>153L:B|PDBID|CHAIN|SEQUENCE
RTDCYGNVNRIDTTGASCKTAKPEGLSYCGVSASKKIAERDLQAMDRYKTIIKKVGEKLCVEPAVIAGIISRESHAGKVL
KNGWGDRGNGFGLMQVDKRSHKPQGTWNGEVHITQGTTILINFIKTIQKKFPSWTKDQQLKGGISAYNAGAGNVRSYARM
DIGTTHDDYANDVVARAQYYKQHGY
>16VP:A|PDBID|CHAIN|SEQUENCE... (7 Replies)
Hello,
I have 10 fasta files with sequenced reads information with read sizes from 15 - 35 . I have combined the reads and collapsed in to unique reads and filtered for sizes 18 - 26 bp long unique reads. Now i wanted to count each unique read appearance in all the fasta files and make a table... (5 Replies)
Hallo,
I need to extract distinct sequence of letters for example from 136 to 193
Files are quite big, so I would prefer not to use "fold -w1"
Thank you very much
Input file look like this:
1 cttttacctt catgtgtttt tgcagatatt tgttcataat aacatcttct ttttaagtta
61 ttaaaatctt... (4 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)