I have a fastq file from small RNA sequencing with sequence lengths between 15 - 30. I wanted to filter sequence lengths between 21-25 and write to another fastq file. how can i do that? (4 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)
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)
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 have this file:
>ID1
AA
>ID2
TTTTTT
>ID-3
AAAAAAAAA
>ID4
TTTTTTGGAGATCAGTAGCAGATGACAG-GGGGG-TGCACCCC
Add I am trying to use this script to output sequences longer than 15 characters:
sed -r '/^>/N;{/^.{,15}$/d}'
The desire output would be this:
>ID4... (8 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)
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
algorithm::diffold
Algorithm::DiffOld(3pm) User Contributed Perl Documentation Algorithm::DiffOld(3pm)NAME
Algorithm::DiffOld - Compute `intelligent' differences between two files / lists but use the old (<=0.59) interface.
NOTE
This has been provided as part of the Algorithm::Diff package by Ned Konz. This particular module is ONLY for people who HAVE to have the
old interface, which uses a comparison function rather than a key generating function.
Because each of the lines in one array have to be compared with each of the lines in the other array, this does M*N comparisions. This can
be very slow. I clocked it at taking 18 times as long as the stock version of Algorithm::Diff for a 4000-line file. It will get worse
quadratically as array sizes increase.
SYNOPSIS
use Algorithm::DiffOld qw(diff LCS traverse_sequences);
@lcs = LCS( @seq1, @seq2, $comparison_function );
$lcsref = LCS( @seq1, @seq2, $comparison_function );
@diffs = diff( @seq1, @seq2, $comparison_function );
traverse_sequences( @seq1, @seq2,
{ MATCH => $callback,
DISCARD_A => $callback,
DISCARD_B => $callback,
},
$comparison_function );
COMPARISON FUNCTIONS
Each of the main routines should be passed a comparison function. If you aren't passing one in, use Algorithm::Diff instead.
These functions should return a true value when two items should compare as equal.
For instance,
@lcs = LCS( @seq1, @seq2, sub { my ($a, $b) = @_; $a eq $b } );
but if that is all you're doing with your comparison function, just use Algorithm::Diff and let it do this (this is its default).
Or:
sub someFunkyComparisonFunction
{
my ($a, $b) = @_;
$a =~ m{$b};
}
@diffs = diff( @lines, @patterns, &someFunkyComparisonFunction );
which would allow you to diff an array @lines which consists of text lines with an array @patterns which consists of regular expressions.
This is actually the reason I wrote this version -- there is no way to do this with a key generation function as in the stock
Algorithm::Diff.
perl v5.10.1 2006-07-31 Algorithm::DiffOld(3pm)