How to add specific bases at the beginning and ending of all the fasta sequences?
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
I need to add the following bases CTGATAGTA at the beginning and ending of every fasta sequences respectively.
I have tried the following command line to add bases at the end of fasta file, but it is not serving my purpose,
. For adding bases at the beginning I do not have any idea, However, I tried the following command
, but its adding bases at the fasta header.
Please help me to do the same.
Thank you.
I have got an Perl array like:
@array = (1,2,3,4,5,6,1,2,3,4,1,2,1,2,3,4,5,6,7,8,9...............)
This numeric sequence will be always sequentially increasing, unless it encounters, The beginning of the new sequentially increasing numeric sequence.
SO in this array we get sequentially... (5 Replies)
Hi, I have multiple large files which consist of the below format:
I am trying to write an awk or sed script to remove all occurrences of the 00 record except the first and remove all of the 80 records except the last one.
Any help would be greatly appreciated. (10 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 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 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)
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
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)