showfeat.txt

emboss的linux版本的源代码

   The feature input is the feature table lines from a normal sequence
   USA.

  Input files for usage example

   'tembl:hsfau1' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:hsfau1

ID   HSFAU1     standard; DNA; HUM; 2016 BP.
XX
AC   X65921; S45242;
XX
SV   X65921.1
XX
DT   13-MAY-1992 (Rel. 31, Created)
DT   21-JUL-1993 (Rel. 36, Last updated, Version 5)
XX
DE   H.sapiens fau 1 gene
XX
KW   fau 1 gene.
XX
OS   Homo sapiens (human)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Primates; Catarrhini; Hominidae; Homo.
XX
RN   [1]
RP   1-2016
RA   Kas K.;
RT   ;
RL   Submitted (29-APR-1992) to the EMBL/GenBank/DDBJ databases.
RL   K. Kas, University of Antwerp, Dept of Biochemistry T3.22,
RL   Universiteitsplein 1, 2610 Wilrijk, BELGIUM
XX
RN   [2]
RP   1-2016
RX   MEDLINE; 92412144.
RA   Kas K., Michiels L., Merregaert J.;
RT   "Genomic structure and expression of the human fau gene: encoding the
RT   ribosomal protein S30 fused to a ubiquitin-like protein.";
RL   Biochem. Biophys. Res. Commun. 187:927-933(1992).
XX
DR   SWISS-PROT; P35544; UBIM_HUMAN.
DR   SWISS-PROT; Q05472; RS30_HUMAN.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..2016
FT                   /db_xref="taxon:9606"
FT                   /organism="Homo sapiens"
FT                   /clone_lib="CML cosmid"
FT                   /clone="15.1"
FT   mRNA            join(408..504,774..856,951..1095,1557..1612,1787..>1912)
FT                   /gene="fau 1"
FT   exon            408..504
FT                   /number=1
FT   intron          505..773
FT                   /number=1
FT   exon            774..856


  [Part of this file has been deleted for brevity]

FT                   RAKRRMQYNRRFVNVVPTFGKKKGPNANS"
FT   intron          857..950
FT                   /number=2
FT   exon            951..1095
FT                   /number=3
FT   intron          1096..1556
FT                   /number=3
FT   exon            1557..1612
FT                   /number=4
FT   intron          1613..1786
FT                   /number=4
FT   exon            1787..>1912
FT                   /number=5
FT   polyA_signal    1938..1943
XX
SQ   Sequence 2016 BP; 421 A; 562 C; 538 G; 495 T; 0 other;
     ctaccatttt ccctctcgat tctatatgta cactcgggac aagttctcct gatcgaaaac        6
0
     ggcaaaacta aggccccaag taggaatgcc ttagttttcg gggttaacaa tgattaacac       12
0
     tgagcctcac acccacgcga tgccctcagc tcctcgctca gcgctctcac caacagccgt       18
0
     agcccgcagc cccgctggac accggttctc catccccgca gcgtagcccg gaacatggta       24
0
     gctgccatct ttacctgcta cgccagcctt ctgtgcgcgc aactgtctgg tcccgccccg       30
0
     tcctgcgcga gctgctgccc aggcaggttc gccggtgcga gcgtaaaggg gcggagctag       36
0
     gactgccttg ggcggtacaa atagcaggga accgcgcggt cgctcagcag tgacgtgaca       42
0
     cgcagcccac ggtctgtact gacgcgccct cgcttcttcc tctttctcga ctccatcttc       48
0
     gcggtagctg ggaccgccgt tcaggtaaga atggggcctt ggctggatcc gaagggcttg       54
0
     tagcaggttg gctgcggggt cagaaggcgc ggggggaacc gaagaacggg gcctgctccg       60
0
     tggccctgct ccagtcccta tccgaactcc ttgggaggca ctggccttcc gcacgtgagc       66
0
     cgccgcgacc accatcccgt cgcgatcgtt tctggaccgc tttccactcc caaatctcct       72
0
     ttatcccaga gcatttcttg gcttctctta caagccgtct tttctttact cagtcgccaa       78
0
     tatgcagctc tttgtccgcg cccaggagct acacaccttc gaggtgaccg gccaggaaac       84
0
     ggtcgcccag atcaaggtaa ggctgcttgg tgcgccctgg gttccatttt cttgtgctct       90
0
     tcactctcgc ggcccgaggg aacgcttacg agccttatct ttccctgtag gctcatgtag       96
0
     cctcactgga gggcattgcc ccggaagatc aagtcgtgct cctggcaggc gcgcccctgg      102
0
     aggatgaggc cactctgggc cagtgcgggg tggaggccct gactaccctg gaagtagcag      108
0
     gccgcatgct tggaggtgag tgagagagga atgttctttg aagtaccggt aagcgtctag      114
0
     tgagtgtggg gtgcatagtc ctgacagctg agtgtcacac ctatggtaat agagtacttc      120
0
     tcactgtctt cagttcagag tgattcttcc tgtttacatc cctcatgttg aacacagacg      126
0
     tccatgggag actgagccag agtgtagttg tatttcagtc acatcacgag atcctagtct      132
0
     ggttatcagc ttccacacta aaaattaggt cagaccaggc cccaaagtgc tctataaatt      138
0
     agaagctgga agatcctgaa atgaaactta agatttcaag gtcaaatatc tgcaactttg      144
0
     ttctcattac ctattgggcg cagcttctct ttaaaggctt gaattgagaa aagaggggtt      150
0
     ctgctgggtg gcaccttctt gctcttacct gctggtgcct tcctttccca ctacaggtaa      156
0
     agtccatggt tccctggccc gtgctggaaa agtgagaggt cagactccta aggtgagtga      162
0
     gagtattagt ggtcatggtg ttaggacttt ttttcctttc acagctaaac caagtccctg      168
0
     ggctcttact cggtttgcct tctccctccc tggagatgag cctgagggaa gggatgctag      174
0
     gtgtggaaga caggaaccag ggcctgatta accttccctt ctccaggtgg ccaaacagga      180
0
     gaagaagaag aagaagacag gtcgggctaa gcggcggatg cagtacaacc ggcgctttgt      186
0
     caacgttgtg cccacctttg gcaagaagaa gggccccaat gccaactctt aagtcttttg      192
0
     taattctggc tttctctaat aaaaaagcca cttagttcag tcatcgcatt gtttcatctt      198
0
     tacttgcaag gcctcaggga gaggtgtgct tctcgg                                201
6
//

Output file format

   The output is a text representation of the feature table.

  Output files for usage example

  File: hsfau1.showfeat

HSFAU1
H.sapiens fau 1 gene
|==========================================================| 2016
|----------------------------------------------------------> source
           |-->                                              exon
           |-->                                              mRNA
              |------->                                      intron
                      |->                                    exon
                      |->                                    mRNA
                      |->                                    CDS
                        |-->                                 intron
                           |--->                             CDS
                           |--->                             exon
                           |--->                             mRNA
                               |------------->               intron
                                             |>              CDS
                                             |>              exon
                                             |>              mRNA
                                               |---->        intron
                                                    |-->     CDS
                                                    |-->     exon
                                                    |-->     mRNA
                                                        >    polyA_signal

  Output files for usage example 2

  File: hsfau1.showfeat

HSFAU1
H.sapiens fau 1 gene
|==========================================================| 2016
|----------------------------------------------------------> 1-2016 source
           |-->       |->  |--->             |>     |-->     408-504,774-856,95
1-1095,1557-1612,1787-1912 mRNA
           |-->                                              408-504 exon
              |------->                                      505-773 intron
                      |->                                    774-856 exon
                      |->  |--->             |>     |-->     782-856,951-1095,1
557-1612,1787-1912 CDS
                        |-->                                 857-950 intron
                           |--->                             951-1095 exon
                               |------------->               1096-1556 intron
                                             |>              1557-1612 exon
                                               |---->        1613-1786 intron
                                                    |-->     1787-1912 exon
                                                        >    1938-1943 polyA_si
gnal

  Output files for usage example 3

  File: hsfau1.showfeat

782-856 CDS
951-1095 CDS
1557-1612 CDS
1787-1912 CDS

Data files

   None.

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with a status of 0.

Known bugs

   None.

See also

   Program name                        Description
   abiview      Reads ABI file and display the trace
   cirdna       Draws circular maps of DNA constructs
   coderet      Extract CDS, mRNA and translations from feature tables
   extractfeat  Extract features from a sequence
   lindna       Draws linear maps of DNA constructs
   maskfeat     Mask off features of a sequence
   pepnet       Displays proteins as a helical net
   pepwheel     Shows protein sequences as helices
   prettyplot   Displays aligned sequences, with colouring and boxing
   prettyseq    Output sequence with translated ranges
   remap        Display sequence with restriction sites, translation etc
   seealso      Finds programs sharing group names
   showalign    Displays a multiple sequence alignment
   showdb       Displays information on the currently available databases
   showseq      Display a sequence with features, translation etc
   sixpack      Display a DNA sequence with 6-frame translation and ORFs
   textsearch   Search sequence documentation. Slow, use SRS and Entrez!
   twofeat      Finds neighbouring pairs of features in sequences

Author(s)

   Gary Williams (gwilliam