How to find a specific sequence pattern in a fasta file?
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,
I have a fasta file as follows,
gene.fasta
The expected output should be like this,
In order to mine the above mentioned pattern, I have used grep command but, I do not know how to specify only 3 bases for Z and also I could not specify N16 criteria in the grep command line. In addition to this, I do not know how to mine the 5 of the flanking bases along with the pattern. So kindly help me in this regard.
Thank you in advance.
Last edited by dineshkumarsrk; 11-29-2019 at 07:15 AM..
A developer of mine has this requirement - I couldn't tell her quickly how to do it with UNIX commands or a quick script so she's writing a quick program to do it - but that got my curiousity up and thought I'd ask here for advice.
In a text file, there are some records (about half of them)... (4 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 all !
I have a fasta file that looks like that:
>Sequence1
RTYIPLCASQHKLCPITFLAVK
(it's just an example, obviously in reality I have several pairs of lines like that)
Using UNIX command(s), would it be possible to replace all the characters except the "C" of the second line only by... (7 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 need assistance with following requirement, I am new to Unix.
I want to do the following task but stuck with file creation date(sysdate)
Following is the requirement
I need to create a script that will read the abc/xyz/klm folder and look for *.err files for that day’s date and then send an... (4 Replies)
Hi,
I want to match the sequence id (sub-string of line starting with '>' and extract the information upto next '>' line ). Please help .
input
> fefrwefrwef X900
AGAGGGAATTGG
AGGGGCCTGGAG
GGTTCTCTTC
> fefrwefrwef X932
AGAGGGAATTGG
AGGAGGTGGAG
GGTTCTCTTC
> fefrwefrwef X937... (2 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)
Hi
This is my first post and I'm just a beginner. So please be nice to me.
I have a couple of html files where a pattern beginning with "http://www.site.com" and ending with "/resource.dat" is present on every 241st line. How do I extract this to a new text file?
I have tried sed -n 241,241p... (13 Replies)
Discussion started by: dejavo
13 Replies
LEARN ABOUT DEBIAN
2ndscore
2NDSCORE(1) User Contributed Documentation 2NDSCORE(1)NAME
2ndscore - find the best hairpin anchored at each position.
SYNOPSIS
2ndscore in.fasta > out.hairpins
DESCRIPTION
For every position in the sequence this will output a line:
-0.6 52 .. 62 TTCCTAAAGGTTCCA GCG CAAAA TGC CATAAGCACCACATT
(score) (start .. end) (left context) (hairpin) (right contenxt)
For positions near the ends of the sequences, the context may be padded with 'x' characters. If no hairpin can be found, the score will be
'None'.
Multiple fasta files can be given and multiple sequences can be in each fasta file. The output for each sequence will be separated by a
line starting with '>' and containing the FASTA description of the sequence.
Because the hairpin scores of the plus-strand and minus-strand may differ (due to GU binding in RNA), by default 2ndscore outputs two sets
of hairpins for every sequence: the FORWARD hairpins and the REVERSE hairpins. All the forward hairpins are output first, and are
identified by having the word 'FORWARD' at the end of the '>' line preceding them. Similarly, the REVERSE hairpins are listed after a '>'
line ending with 'REVERSE'. If you want to search only one or the other strand, you can use:
--no-fwd Don't print the FORWARD hairpins
--no-rvs Don't print the REVERSE hairpins
You can set the energy function used, just as with transterm with the --gc, --au, --gu, --mm, --gap options. The --min-loop, --max-loop,
and --max-len options are also supported.
FORMAT OF THE .BAG FILES
The columns for the .bag files are, in order:
1. gene_name
2. terminator_start
3. terminator_end
4. hairpin_score
5. tail_score
6. terminator_sequence
7. terminator_confidence: a combination of the hairpin and tail score that
takes into account how likely such scores are in a random sequence. This
is the main "score" for the terminator and is computed as described in
the paper.
8. APPROXIMATE_distance_from_end_of_gene: The *approximate* number of base
pairs between the end of the gene and the start of the terminator. This
is approximate in several ways: First, (and most important) TransTermHP
doesn't always use the real gene ends. Depending on the options you give
it may trim some off the ends of genes to handle terminators that
partially overlap with genes. Second, where the terminator "begins"
isn't that well defined. This field is intended only for a sanity check
(terminators reported to be the best near the ends of genes shouldn't be
_too far_ from the end of the gene).
USING TRANSTERM WITHOUT GENOME ANNOTATIONS
TransTermHP uses known gene information for only 3 things: (1) tagging the putative terminators as either "inside genes" or "intergenic,"
(2) choosing the background GC-content percentage to compute the scores, because genes often have different GC content than the intergenic
regions, and (3) producing slightly more readable output. Items (1) and (3) are not really necessary, and (2) has no effect if your genes
have about the same GC-content as your intergenic regions.
Unfortunately, TransTermHP doesn't yet have a simple option to run without an annotation file (either .ptt or .coords), and requires at
least 2 genes to be present. The solution is to create fake, small genes that flank each chromosome. To do this, make a fake.coords file
that contains only these two lines:
fakegene1 1 2 chome_id
fakegene2 L-1 L chrom_id
where L is the length of the input sequence and L-1 is 1 less than the length of the input sequence. "chrom_id" should be the word directly
following the ">" in the .fasta file containing your sequence. (If, for example, your .fasta file began with ">seq1", then chrom_id =
seq1).
This creates a "fake" annotation with two 1-base-long genes flanking the sequence in a tail-to-tail arrangement: --> <--. TransTermHP can
then be run with:
transterm -p expterm.dat sequence.fasta fake.coords
If the G/C content of your intergenic regions is about the same as your genes, then this won't have too much of an effect on the scores
terminators receive. On the other hand, this use of TransTermHP hasn't been tested much at all, so it's hard to vouch for its accuracy.
SEE ALSO transterm(1)AUTHOR
Alex Mestiashvili <alex@biotec.tu-dresden.de>
2011-02-19 2NDSCORE(1)