Hopefully someone here can point me in the correct direction.
I'm working on a username migration and am trying to map my users ols usernames to the new ones.
Right now every user has a username of firstname.lastname i.e. john.doe
I'm trying to create a bash or python script that will take... (3 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 need some help with modifying fasta headers.
I have a fasta file with thousands of contigs and I need to modify their headers with the information obtained from a second file.
File 1 contains the fasta sequences:
>contig0001 length=11115 numreads=10777
agatgtagatctct... (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've been struggling with this one for quite a while and cannot seem to find a solution for this find/replace scenario. Perhaps I'm getting rusty.
I have a file that contains a number of metrics (exactly 3 fields per line) from a few appliances that are collected in parallel. To identify the... (3 Replies)
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
test.fasta
>TalAA18_Xoo_CIAT_NZ_CP033194.1:_2936369-2939570:+1... (1 Reply)
Discussion started by: dineshkumarsrk
1 Replies
LEARN ABOUT DEBIAN
tfbs::patterngen::simplepfm
TFBS::PatternGen::SimplePFM(3pm) User Contributed Perl Documentation TFBS::PatternGen::SimplePFM(3pm)NAME
TFBS::PatternGen::SimplePFM - a simple position frequency matrix factory
SYNOPSIS
my @sequences = qw( AAGCCT AGGCAT AAGCCT
AAGCCT AGGCAT AGGCCT
AGGCAT AGGTTT AGGCAT
AGGCCT AGGCCT );
my $patterngen =
TFBS::PatternGen::SimplePFM->new(-seq_list=>@sequences);
my $pfm = $patterngen->pattern(); # $pfm is now a TFBS::Matrix::PFM object
DESCRIPTION
TFBS::PatternGen::SimplePFM generates a position frequency matrix from a set of nucleotide sequences of equal length, The sequences can be
passed either as strings, as Bio::Seq objects or as a fasta file.
This pattern generator always creates only one pattern from a given set of sequences.
new
Title : new
Usage : my $db = TFBS::PatternGen::SimplePFM->new(%args);
Function: the constructor for the TFBS::PatternGen::SimplePFM
object
Returns : a TFBS::PatternGen::SimplePFM obkect
Args : This method takes named arguments;
you must specify one of the following
-seq_list # a reference to an array of strings
# and/or Bio::Seq objects
# or
-seq_stream # A Bio::SeqIO object
# or
-seq_file # the name of the fasta file containing
# all the sequences
pattern
all_patterns
patternSet
The three above methods are used fro the retrieval of patterns, and are common to all TFBS::PatternGen::* classes. Please see
TFBS::PatternGen for details.
perl v5.14.2 2008-01-24 TFBS::PatternGen::SimplePFM(3pm)