Hello All - I am looking for help on how to solve a re-occuring problem. I have a file with certain sequences in it that need to be removed. The sequences are always different but the fix is always the same remove those sequences and leave the rest. Another team ID's the bad sequences and then I... (3 Replies)
Hey,
I've been trying to break a massive fasta formatted file into files containing each gene separately. Could anyone help me? I've tried to use the following code but i've recieved errors every time:
for i in *.rtf.out
do
awk '/^>/{f=++d".fasta"} {print > $i.out}' $i
done (1 Reply)
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)
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)
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 MOJAVE
algorithm::diffold
Algorithm::DiffOld(3) User Contributed Perl Documentation Algorithm::DiffOld(3)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 v5.18.2 2006-07-30 Algorithm::DiffOld(3)