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trimseq |
Function
Trim ambiguous bits off the ends of sequencesDescription
This program is used to tidy up the ends of sequences, removing all the bits that you would really rather were not published.Specifically, it:
- removes all gap characters from the ends.
- removes X's and N's (in nucleic sequences) from the ends.
- optionally removes *'s from the ends
- optionally removes IUPAC ambiguity codes from the ends (B and Z in proteins, M,R,W,S,Y,K,V,H,D and B in nucleic sequences)
It then optionally trims off poor quality regions from the end, using a threshold percentage of unwanted characters in a window which is moved along the sequence from the ends. The unwanted characters which are used are X's and N's (in nucleic sequences), optionally *'s, and optionally IUPAC ambiguity codes.
The program stops trimming the ends when the percentage of unwanted characters in the moving window drops below the threshold percentage.
Thus if the window size is set to 1 and the percentage threshold is 100, no further poor quality regions will be removed. If the window size is set to 5 and the percentage threshold is 40 then the sequence AAGCTNNNNATT will be trimmed to AAGCT, while AAGCTNATT or AAGCTNNNNATTT will not be trimmed as less than 40% of the last 5 characters are N's.
After trimming these poor quality regions, it will again then trim off any dangling gap characters from the ends .
Usage
Here is a sample session with trimseq
% trimseq tembl:hsfau hsfau.seq -window 1 -percent 100 Trim ambiguous bits off the ends of sequences |
Go to the input files for this example
Go to the output files for this example
Example 2
% trimseq tembl:hsfau hsfau.seq -window 5 -percent 40 Trim ambiguous bits off the ends of sequences |
Example 3
% trimseq tembl:hsfau hsfau.seq -window 20 -percent 80 Trim ambiguous bits off the ends of sequences |
Example 4
% trimseq tembl:hsfau hsfau.seq -window 20 -percent 10 Trim ambiguous bits off the ends of sequences |
Example 5
% trimseq tembl:hsfau hsfau.seq -window 20 -percent 50 -strict Trim ambiguous bits off the ends of sequences |
Example 6
% trimseq tembl:hsfau hsfau.seq -window 1 -percent 100 -star Trim ambiguous bits off the ends of sequences |
Example 7
% trimseq tembl:hsfau hsfau.seq -window 20 -percent 50 -noright Trim ambiguous bits off the ends of sequences |
Command line arguments
Standard (Mandatory) qualifiers:
[-sequence] seqall Sequence database USA
[-outseq] seqoutall Output sequence(s) USA
Additional (Optional) qualifiers:
-window integer This determines the size of the region that
is considered when deciding whether the
percentage of ambiguity is greater than the
threshold. A value of 5 means that a region
of 5 letters in the sequence is shifted
along the sequence from the ends and
trimming is done only if there is a greater
or equal percentage of ambiguity than the
threshold percentage.
-percent float This is the threshold of the percentage
ambiguity in the window required in order to
trim a sequence.
-strict boolean In nucleic sequences, trim off not only N's
and X's, but also the nucleotide IUPAC
ambiguity codes M, R, W, S, Y, K, V, H, D
and B. In protein sequences, trim off not
only X's but also B and Z.
-star boolean In protein sequences, trim off not only X's,
but also the *'s
Advanced (Unprompted) qualifiers:
-[no]left boolean Trim at the start
-[no]right boolean Trim at the end
Associated qualifiers:
"-sequence" associated qualifiers
-sbegin1 integer Start of each sequence to be used
-send1 integer End of each sequence to be used
-sreverse1 boolean Reverse (if DNA)
-sask1 boolean Ask for begin/end/reverse
-snucleotide1 boolean Sequence is nucleotide
-sprotein1 boolean Sequence is protein
-slower1 boolean Make lower case
-supper1 boolean Make upper case
-sformat1 string Input sequence format
-sdbname1 string Database name
-sid1 string Entryname
-ufo1 string UFO features
-fformat1 string Features format
-fopenfile1 string Features file name
"-outseq" associated qualifiers
-osformat2 string Output seq format
-osextension2 string File name extension
-osname2 string Base file name
-osdirectory2 string Output directory
-osdbname2 string Database name to add
-ossingle2 boolean Separate file for each entry
-oufo2 string UFO features
-offormat2 string Features format
-ofname2 string Features file name
-ofdirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write standard output
-filter boolean Read standard input, write standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report deaths
|
| Standard (Mandatory) qualifiers | Allowed values | Default | |
|---|---|---|---|
| [-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
| [-outseq] (Parameter 2) |
Output sequence(s) USA | Writeable sequence(s) | <sequence>.format |
| Additional (Optional) qualifiers | Allowed values | Default | |
| -window | This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage. | Any integer value | 1 |
| -percent | This is the threshold of the percentage ambiguity in the window required in order to trim a sequence. | Any numeric value | 100.0 |
| -strict | In nucleic sequences, trim off not only N's and X's, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B. In protein sequences, trim off not only X's but also B and Z. | Boolean value Yes/No | No |
| -star | In protein sequences, trim off not only X's, but also the *'s | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | Allowed values | Default | |
| -[no]left | Trim at the start | Boolean value Yes/No | Yes |
| -[no]right | Trim at the end | Boolean value Yes/No | Yes |
Input file format
Normal sequence.Input files for usage example
'tembl:hsfau' is a sequence entry in the example nucleic acid database 'tembl'
Database entry: tembl:hsfau
ID HSFAU standard; RNA; HUM; 518 BP.
XX
AC X65923;
XX
SV X65923.1
XX
DT 13-MAY-1992 (Rel. 31, Created)
DT 23-SEP-1993 (Rel. 37, Last updated, Version 10)
XX
DE H.sapiens fau mRNA
XX
KW fau gene.
XX
OS Homo sapiens (human)
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN [1]
RP 1-518
RA Michiels L.M.R.;
RT ;
RL Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL L.M.R. Michiels, University of Antwerp, Dept of Biochemistry,
RL Universiteisplein 1, 2610 Wilrijk, BELGIUM
XX
RN [2]
RP 1-518
RX MEDLINE; 93368957.
RA Michiels L., Van der Rauwelaert E., Van Hasselt F., Kas K., Merregaert J.;
RT " fau cDNA encodes a ubiquitin-like-S30 fusion protein and is expressed as
RT an antisense sequences in the Finkel-Biskis-Reilly murine sarcoma virus";
RL Oncogene 8:2537-2546(1993).
XX
DR SWISS-PROT; P35544; UBIM_HUMAN.
DR SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH Key Location/Qualifiers
FH
FT source 1..518
FT /chromosome="11q"
FT /db_xref="taxon:9606"
FT /organism="Homo sapiens"
FT /tissue_type="placenta"
FT /clone_lib="cDNA"
FT /clone="pUIA 631"
FT /map="13"
FT misc_feature 57..278
FT /note="ubiquitin like part"
FT CDS 57..458
FT /db_xref="SWISS-PROT:P35544"
FT /db_xref="SWISS-PROT:Q05472"
FT /gene="fau"
FT /protein_id="CAA46716.1"
FT /translation="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLAG
FT APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKTG
FT RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT misc_feature 98..102
FT /note="nucleolar localization signal"
FT misc_feature 279..458
FT /note="S30 part"
FT polyA_signal 484..489
FT polyA_site 509
XX
SQ Sequence 518 BP; 125 A; 139 C; 148 G; 106 T; 0 other;
ttcctctttc tcgactccat cttcgcggta gctgggaccg ccgttcagtc gccaatatgc 60
agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg 120
cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc 180
tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc 240
tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc 300
gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga 360
agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca 420
cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc 480
tctaataaaa aagccactta gttcagtcaa aaaaaaaa 518
//
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Output file format
Normal sequence file.Output files for usage example
File: hsfau.seq
>HSFAU X65923.1 H.sapiens fau mRNA ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttcagtcaaaaaaaaaa |
Data files
None.Notes
If you use the '-star' qualifier and set the window size to greater than 1, you may trim bits of sequence with internal *'s. This may not be what you expected.References
None.Warnings
None.Diagnostic Error Messages
None.Exit status
It always exits with status 0.Known bugs
None noted.See also
| Program name | Description |
|---|---|
| biosed | Replace or delete sequence sections |
| codcopy | Reads and writes a codon usage table |
| cutseq | Removes a specified section from a sequence |
| degapseq | Removes gap characters from sequences |
| descseq | Alter the name or description of a sequence |
| entret | Reads and writes (returns) flatfile entries |
| extractfeat | Extract features from a sequence |
| extractseq | Extract regions from a sequence |
| listor | Write a list file of the logical OR of two sets of sequences |
| maskfeat | Mask off features of a sequence |
| maskseq | Mask off regions of a sequence |
| newseq | Type in a short new sequence |
| noreturn | Removes carriage return from ASCII files |
| notseq | Exclude a set of sequences and write out the remaining ones |
| nthseq | Writes one sequence from a multiple set of sequences |
| pasteseq | Insert one sequence into another |
| revseq | Reverse and complement a sequence |
| seqret | Reads and writes (returns) sequences |
| seqretsplit | Reads and writes (returns) sequences in individual files |
| skipseq | Reads and writes (returns) sequences, skipping first few |
| splitter | Split a sequence into (overlapping) smaller sequences |
| trimest | Trim poly-A tails off EST sequences |
| union | Reads sequence fragments and builds one sequence |
| vectorstrip | Strips out DNA between a pair of vector sequences |
| yank | Reads a sequence range, appends the full USA to a list file |
Author(s)
Gary Williams (gwilliam © rfcgr.mrc.ac.uk)MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SB, UK