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trimest reads one or more nucleotide sequences and writes them out again but with any 3' poly-A tail (or, optionally, 5' poly-T tail) removed. It detect any poly-A and poly-T tails in the input sequences that are at least the specified minimum length. The tails may continue a defined num of non-A or non-T bases. If both a 5' poly-T tail and a 3' poly-A tail is identified, it removes the longest of the two. The output is a set of sequences with the poly-A (or poly-T) tails removed. If a sequence had a 5' poly-T tail then the resulting sequence is reverse-complemented by default. The description line has a comment appended about the changes made to the sequence.
trimest looks for a repeat of at least -minlength A's at the 3' end (and, by default, -minlength T's at the 5' end). If there are an apparent 5' poly-T tail and a poly-A tail, then it removes whichever is the longer of the two.
By default, it will allow -mismatches non-A (or non-T) bases in the tail. If a mismatch is found, then there has to be at least -minlength A's (or T's) past the mismatch (working from the end) for the mismatch to be considered part of the tail. If -mismatches is greater than 1 then that number of contiguous non-A (or non-T) bases will be allowed as part of the tail.
% trimest tembl:x65923 x65923.seq Remove poly-A tails from nucleotide sequences
Go to the input files for this example
Go to the output files for this example
Standard (Mandatory) qualifiers: [-sequence] seqall Nucleotide sequence(s) filename and optional format, or reference (input USA) [-outseq] seqoutall [
|Standard (Mandatory) qualifiers||Allowed values||Default|
|Nucleotide sequence(s) filename and optional format, or reference (input USA)||Readable sequence(s)||Required|
|Sequence set(s) filename and optional format (output USA)||Writeable sequence(s)||<*>.format|
|Additional (Optional) qualifiers||Allowed values||Default|
|-minlength||This is the minimum length that a poly-A (or poly-T) tail must have before it is removed. If there are mismatches in the tail than there must be at least this length of poly-A tail before the mismatch for the mismatch to be considered part of the tail.||Integer 1 or more||4|
|-mismatches||If there are this number or fewer contiguous non-A bases in a poly-A tail then, if there are '-minlength' 'A' bases before them, they will be considered part of the tail and removed . For example the terminal 4 A's of GCAGAAAA would be removed with the default values of -minlength=4 and -mismatches=1 (There are not at least 4 A's before the last 'G' and so only the A's after it are considered to be part of the tail). The terminal 9 bases of GCAAAAGAAAA would be removed; There are at least -minlength A's preceeding the last 'G', so it is part of the tail.||Integer 0 or more||1|
|-[no]reverse||When a poly-T region at the 5' end of the sequence is found and removed, it is likely that the sequence is in the reverse sense. This option will change the sequence to the forward sense when it is written out. If this option is not set, then the sense will not be changed.||Boolean value Yes/No||Yes|
|-tolower||The poly-A region can be 'masked' by converting the sequence characters to lower-case. Some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the '-supper' sequence qualifier.||Toggle value Yes/No||No|
|Advanced (Unprompted) qualifiers||Allowed values||Default|
|-[no]fiveprime||If this is set true, then the 5' end of teh sequence is inspected for poly-T tails. These will be removed if they are longer than any 3' poly-A tails. If this is false, then the 5' end is ignored.||Boolean value Yes/No||Yes|
ID X65923; SV 1; linear; mRNA; STD; HUM; 518 BP. XX AC X65923; XX DT 13-MAY-1992 (Rel. 31, Created) DT 18-APR-2005 (Rel. 83, Last updated, Version 11) 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; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Homo. XX RN  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  RP 1-518 RX PUBMED; 8395683. 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 sequence in the Finkel-Biskis-Reilly murine sarcoma virus"; RL Oncogene 8(9):2537-2546(1993). XX DR H-InvDB; HIT000322806. XX FH Key Location/Qualifiers FH FT source 1..518 FT /organism="Homo sapiens" FT /chromosome="11q" FT /map="13" FT /mol_type="mRNA" FT /clone_lib="cDNA" FT /clone="pUIA 631" FT /tissue_type="placenta" FT /db_xref="taxon:9606" FT misc_feature 57..278 FT /note="ubiquitin like part" FT CDS 57..458 FT /gene="fau" FT /db_xref="GDB:135476" FT /db_xref="GOA:P62861" FT /db_xref="HGNC:3597" FT /db_xref="HSSP:1GJZ" FT /db_xref="InterPro:IPR006846" FT /db_xref="UniProtKB/Swiss-Prot:P35544" 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 //
If a poly-A tail is reomved then [poly-A tail removed] is appended to the description of the sequence. If poly-T is removed, then [poly-T tail removed] is appended and if the sequence is reversed, [reverse complement] is appended.
>X65923 X65923.1 H.sapiens fau mRNA [poly-A tail removed] ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtcgccaatatgc agctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacggtcg cccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgc tcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccc tgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaagaaga agacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtgccca cctttggcaagaagaagggccccaatgccaactcttaagtcttttgtaattctggctttc tctaataaaaaagccacttagttcagtc
The output is a set of sequences with the poly-A (or poly-T) tails removed. If a sequence had a 5' poly-T tail then the resulting sequence is reverse-complemented by default. The description line has a comment appended about the changes made to the sequence.
EST and mRNA sequences often have poly-A tails at their 3' end. Where an EST sequences is the reverse complement of a corresponding mRNA's forward sense it may have a poly-T tail at its 5' end.
trimest is not infallible. There are often repeats of A (or T) in a sequence that just happen by chance to occur at the 3' (or 5') end of the EST sequence. trimest has no way of determining if the A's it finds are part of a real poly-A tail or are a part of the transcribed genomic sequence. It removes any apparent poly-A tails that match its criteria for a poly-A tail (see "Algorithm").
trimest can make no guarantee that the tails removed have biologic significance or not. They may in fact be part of the transcribed sequence.
|aligncopy||Reads and writes alignments|
|aligncopypair||Reads and writes pairs from alignments|
|biosed||Replace or delete sequence sections|
|codcopy||Copy and reformat a codon usage table|
|cutseq||Removes a section from a sequence|
|degapseq||Removes non-alphabetic (e.g. gap) characters from sequences|
|descseq||Alter the name or description of a sequence|
|entret||Retrieves sequence entries from flatfile databases and files|
|extractalign||Extract regions from a sequence alignment|
|extractfeat||Extract features from sequence(s)|
|extractseq||Extract regions from a sequence|
|featcopy||Reads and writes a feature table|
|featreport||Reads and writes a feature table|
|listor||Write a list file of the logical OR of two sets of sequences|
|makenucseq||Create random nucleotide sequences|
|makeprotseq||Create random protein sequences|
|maskambignuc||Masks all ambiguity characters in nucleotide sequences with N|
|maskambigprot||Masks all ambiguity characters in protein sequences with X|
|maskfeat||Write a sequence with masked features|
|maskseq||Write a sequence with masked regions|
|newseq||Create a sequence file from a typed-in sequence|
|nohtml||Remove mark-up (e.g. HTML tags) from an ASCII text file|
|noreturn||Remove carriage return from ASCII files|
|nospace||Remove all whitespace from an ASCII text file|
|notab||Replace tabs with spaces in an ASCII text file|
|notseq||Write to file a subset of an input stream of sequences|
|nthseq||Write to file a single sequence from an input stream of sequences|
|nthseqset||Reads and writes (returns) one set of sequences from many|
|pasteseq||Insert one sequence into another|
|revseq||Reverse and complement a nucleotide sequence|
|seqret||Reads and writes (returns) sequences|
|seqretsetall||Reads and writes (returns) many sets of sequences|
|seqretsplit||Reads sequences and writes them to individual files|
|sizeseq||Sort sequences by size|
|skipredundant||Remove redundant sequences from an input set|
|skipseq||Reads and writes (returns) sequences, skipping first few|
|splitsource||Split sequence(s) into original source sequences|
|splitter||Split sequence(s) into smaller sequences|
|trimseq||Remove unwanted characters from start and end of sequence(s)|
|trimspace||Remove extra whitespace from an ASCII text file|
|union||Concatenate multiple sequences into a single sequence|
|vectorstrip||Removes vectors from the ends of nucleotide sequence(s)|
|yank||Add a sequence reference (a full USA) to a list file|