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entret |
The difference between entret and such programs as seqret which also read entries from databases or files and write them to files, is that entret reads and writes the complete sequence entry together with the heading annotation (documentation). entret therefore is very useful for looking at the annotation of sequences from databases, which seqret does not provide.
The other main difference is that when it writes out the sequence entry to a file, the information is treated as text, not sequence, and so options that you would normally use to change the aspects of the sequence to be written will either not be recognised and will cause an error message to be written (e.g. '-osformat') or will be quietly ignored (e.g. '-sbegin', '-send').
If you have defined a database to use GCG indexed databases, then entret will currently only return the annotation and not the sequence. entret will currently only reproduce the original entry, including the sequence, for databases which hold the whole entry in one file (e.g. the original flatfiles or SRS indexed databases).
% entret embl:hsfau Reads and writes (returns) flatfile entries Output file [hsfau.entret]:
Mandatory qualifiers: [-sequence] seqall Sequence database USA [-outfile] outfile Output file name Optional qualifiers: (none) Advanced qualifiers: -firstonly boolean Read one sequence and stop General qualifiers: -help boolean Report command line options. More information on associated and general qualifiers can be found with -help -verbose |
Mandatory qualifiers | Allowed values | Default | |
---|---|---|---|
[-sequence] (Parameter 1) |
Sequence database USA | Readable sequence(s) | Required |
[-outfile] (Parameter 2) |
Output file name | Output file | <sequence>.entret |
Optional qualifiers | Allowed values | Default | |
(none) | |||
Advanced qualifiers | Allowed values | Default | |
-firstonly | Read one sequence and stop | Yes/No | No |
% more hsfau.entret 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 //
Program name | Description |
---|---|
biosed | Replace or delete sequence sections |
cutseq | Removes a specified section from a sequence |
degapseq | Removes gap characters from sequences |
descseq | Alter the name or description of a sequence |
extractfeat | Extract features from a sequence |
extractseq | Extract regions from a sequence |
listor | Writes 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 | Excludes a set of sequences and writes 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 the first few |
splitter | Split a sequence into (overlapping) smaller sequences |
swissparse | Retrieves sequences from swissprot using keyword search |
trimest | Trim poly-A tails off EST sequences |
trimseq | Trim ambiguous bits off the ends of 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 |