sirna.txt

emboss的linux版本的源代码

   Advanced (Unprompted) qualifiers: (none)
   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

   "-outfile" associated qualifiers
   -rformat2           string     Report format
   -rname2             string     Base file name
   -rextension2        string     File name extension
   -rdirectory2        string     Output directory
   -raccshow2          boolean    Show accession number in the report
   -rdesshow2          boolean    Show description in the report
   -rscoreshow2        boolean    Show the score in the report
   -rusashow2          boolean    Show the full USA in the report
   -rmaxall2           integer    Maximum total hits to report
   -rmaxseq2           integer    Maximum hits to report for one sequence

   "-outseq" associated qualifiers
   -osformat3          string     Output seq format
   -osextension3       string     File name extension
   -osname3            string     Base file name
   -osdirectory3       string     Output directory
   -osdbname3          string     Database name to add
   -ossingle3          boolean    Separate file for each entry
   -oufo3              string     UFO features
   -offormat3          string     Features format
   -ofname3            string     Features file name
   -ofdirectory3       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 dying program messages

Input file format

   sirna reads any normal sequence USAs.

  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="MQLFVRAQELHTFEVTGQETVAQIKAHVASLEGIAPEDQVVLLA
G
FT                   APLEDEATLGQCGVEALTTLEVAGRMLGGKVHGSLARAGKVRGQTPKVAKQEKKKKKT
G
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        6
0
     agctctttgt ccgcgcccag gagctacaca ccttcgaggt gaccggccag gaaacggtcg       12
0
     cccagatcaa ggctcatgta gcctcactgg agggcattgc cccggaagat caagtcgtgc       18
0
     tcctggcagg cgcgcccctg gaggatgagg ccactctggg ccagtgcggg gtggaggccc       24
0
     tgactaccct ggaagtagca ggccgcatgc ttggaggtaa agttcatggt tccctggccc       30
0
     gtgctggaaa agtgagaggt cagactccta aggtggccaa acaggagaag aagaagaaga       36
0
     agacaggtcg ggctaagcgg cggatgcagt acaaccggcg ctttgtcaac gttgtgccca       42
0
     cctttggcaa gaagaagggc cccaatgcca actcttaagt cttttgtaat tctggctttc       48
0
     tctaataaaa aagccactta gttcagtcaa aaaaaaaa                               51
8
//

Output file format

   The output is a standard EMBOSS report file.

   The results can be output in one of several styles by using the
   command-line qualifier -rformat xxx, where 'xxx' is replaced by the
   name of the required format. The available format names are: embl,
   genbank, gff, pir, swiss, trace, listfile, dbmotif, diffseq, excel,
   feattable, motif, regions, seqtable, simple, srs, table, tagseq

   See: http://emboss.sf.net/docs/themes/ReportFormats.html for further
   information on report formats.

   sirna outputs a report format file. The default format is 'table'

  Output files for usage example

  File: hsfau.sirna

########################################
# Program: sirna
# Rundate: Sat 15 Jul 2006 12:00:00
# Commandline: sirna
#    -sequence tembl:hsfau
# Report_format: table
# Report_file: hsfau.sirna
########################################

#=======================================
#
# Sequence: HSFAU     from: 1   to: 518
# HitCount: 85
#
# CDS region found in feature table starting at 57
#
#=======================================

  Start     End   Score    GC% Sense_siRNA Antisense_siRNA
    308     330   9.000   50.0 AAGUGAGAGGUCAGACUCCdTdT GGAGUCUGACCUCUCACUUdTdT
    309     331   9.000   50.0 AGUGAGAGGUCAGACUCCUdTdT AGGAGUCUGACCUCUCACUdTdT
    310     332   9.000   50.0 GUGAGAGGUCAGACUCCUAdTdT UAGGAGUCUGACCUCUCACdTdT
    351     373   9.000   50.0 GAAGAAGAAGACAGGUCGGdTdT CCGACCUGUCUUCUUCUUCdTdT
    166     188   8.000   55.0 GAUCAAGUCGUGCUCCUGGdTdT CCAGGAGCACGACUUGAUCdTdT
    279     301   8.000   55.0 AGUUCAUGGUUCCCUGGCCdTdT GGCCAGGGAACCAUGAACUdTdT
    330     352   8.000   55.0 GGUGGCCAAACAGGAGAAGdTdT CUUCUCCUGUUUGGCCACCdTdT
    354     376   8.000   55.0 GAAGAAGACAGGUCGGGCUdTdT AGCCCGACCUGUCUUCUUCdTdT
    357     379   8.000   55.0 GAAGACAGGUCGGGCUAAGdTdT CUUAGCCCGACCUGUCUUCdTdT
    393     415   8.000   55.0 CCGGCGCUUUGUCAACGUUdTdT AACGUUGACAAAGCGCCGGdTdT
    253     275   7.000   60.0 GUAGCAGGCCGCAUGCUUGdTdT CAAGCAUGCGGCCUGCUACdTdT
    280     302   7.000   60.0 GUUCAUGGUUCCCUGGCCCdTdT GGGCCAGGGAACCAUGAACdTdT
    339     361   7.000   40.0 ACAGGAGAAGAAGAAGAAGdTdT CUUCUUCUUCUUCUCCUGUdTdT
    340     362   7.000   40.0 CAGGAGAAGAAGAAGAAGAdTdT UCUUCUUCUUCUUCUCCUGdTdT
    348     370   7.000   40.0 GAAGAAGAAGAAGACAGGUdTdT ACCUGUCUUCUUCUUCUUCdTdT
    375     397   7.000   60.0 GCGGCGGAUGCAGUACAACdTdT GUUGUACUGCAUCCGCCGCdTdT
    408     430   7.000   60.0 CGUUGUGCCCACCUUUGGCdTdT GCCAAAGGUGGGCACAACGdTdT
    429     451   7.000   60.0 GAAGAAGGGCCCCAAUGCCdTdT GGCAUUGGGGCCCUUCUUCdTdT
    432     454   7.000   60.0 GAAGGGCCCCAAUGCCAACdTdT GUUGGCAUUGGGGCCCUUCdTdT
    435     457   7.000   60.0 GGGCCCCAAUGCCAACUCUdTdT AGAGUUGGCAUUGGGGCCCdTdT
    488     510   7.000   40.0 AAAGCCACUUAGUUCAGUCdTdT GACUGAACUAAGUGGCUUUdTdT
    489     511   7.000   40.0 AAGCCACUUAGUUCAGUCAdTdT UGACUGAACUAAGUGGCUUdTdT
    490     512   7.000   40.0 AGCCACUUAGUUCAGUCAAdTdT UUGACUGAACUAAGUGGCUdTdT
    491     513   7.000   40.0 GCCACUUAGUUCAGUCAAAdTdT UUUGACUGAACUAAGUGGCdTdT
    129     151   6.000   55.0 GGCUCAUGUAGCCUCACUGdTdT CAGUGAGGCUACAUGAGCCdTdT
    165     187   6.000   50.0 AGAUCAAGUCGUGCUCCUGdTdT CAGGAGCACGACUUGAUCUdTdT
    278     300   6.000   50.0 AAGUUCAUGGUUCCCUGGCdTdT GCCAGGGAACCAUGAACUUdTdT
    314     336   6.000   50.0 GAGGUCAGACUCCUAAGGUdTdT ACCUUAGGAGUCUGACCUCdTdT
    321     343   6.000   50.0 GACUCCUAAGGUGGCCAAAdTdT UUUGGCCACCUUAGGAGUCdTdT
    323     345   6.000   50.0 CUCCUAAGGUGGCCAAACAdTdT UGUUUGGCCACCUUAGGAGdTdT
    329     351   6.000   50.0 AGGUGGCCAAACAGGAGAAdTdT UUCUCCUGUUUGGCCACCUdTdT


  [Part of this file has been deleted for brevity]

    353     375   5.000   55.0 AGAAGAAGACAGGUCGGGCdTdT GCCCGACCUGUCUUCUUCUdTdT
    360     382   5.000   65.0 GACAGGUCGGGCUAAGCGGdTdT CCGCUUAGCCCGACCUGUCdTdT
    374     396   5.000   55.0 AGCGGCGGAUGCAGUACAAdTdT UUGUACUGCAUCCGCCGCUdTdT
    383     405   5.000   55.0 UGCAGUACAACCGGCGCUUdTdT AAGCGCCGGUUGUACUGCAdTdT
    387     409   5.000   55.0 GUACAACCGGCGCUUUGUCdTdT GACAAAGCGCCGGUUGUACdTdT
    390     412   5.000   55.0 CAACCGGCGCUUUGUCAACdTdT GUUGACAAAGCGCCGGUUGdTdT
    392     414   5.000   55.0 ACCGGCGCUUUGUCAACGUdTdT ACGUUGACAAAGCGCCGGUdTdT
    407     429   5.000   55.0 ACGUUGUGCCCACCUUUGGdTdT CCAAAGGUGGGCACAACGUdTdT
    428     450   5.000   55.0 AGAAGAAGGGCCCCAAUGCdTdT GCAUUGGGGCCCUUCUUCUdTdT
    431     453   5.000   55.0 AGAAGGGCCCCAAUGCCAAdTdT UUGGCAUUGGGGCCCUUCUdTdT
    434     456   5.000   60.0 AGGGCCCCAAUGCCAACUCdTdT GAGUUGGCAUUGGGGCCCUdTdT
    444     466   5.000   35.0 UGCCAACUCUUAAGUCUUUdTdT AAAGACUUAAGAGUUGGCAdTdT
    487     509   5.000   35.0 AAAAGCCACUUAGUUCAGUdTdT ACUGAACUAAGUGGCUUUUdTdT
    123     145   4.000   50.0 GAUCAAGGCUCAUGUAGCCdTdT GGCUACAUGAGCCUUGAUCdTdT
    125     147   4.000   50.0 UCAAGGCUCAUGUAGCCUCdTdT GAGGCUACAUGAGCCUUGAdTdT
    128     150   4.000   50.0 AGGCUCAUGUAGCCUCACUdTdT AGUGAGGCUACAUGAGCCUdTdT
    155     177   4.000   50.0 UUGCCCCGGAAGAUCAAGUdTdT ACUUGAUCUUCCGGGGCAAdTdT
    234     256   4.000   60.0 GGCCCUGACUACCCUGGAAdTdT UUCCAGGGUAGUCAGGGCCdTdT
    259     281   4.000   60.0 GGCCGCAUGCUUGGAGGUAdTdT UACCUCCAAGCAUGCGGCCdTdT
    266     288   4.000   40.0 UGCUUGGAGGUAAAGUUCAdTdT UGAACUUUACCUCCAAGCAdTdT
    342     364   4.000   40.0 GGAGAAGAAGAAGAAGAAGdTdT CUUCUUCUUCUUCUUCUCCdTdT
    347     369   4.000   40.0 AGAAGAAGAAGAAGACAGGdTdT CCUGUCUUCUUCUUCUUCUdTdT
    359     381   4.000   60.0 AGACAGGUCGGGCUAAGCGdTdT CGCUUAGCCCGACCUGUCUdTdT
    111     133   3.000   55.0 AACGGUCGCCCAGAUCAAGdTdT CUUGAUCUGGGCGACCGUUdTdT
    113     135   3.000   65.0 CGGUCGCCCAGAUCAAGGCdTdT GCCUUGAUCUGGGCGACCGdTdT
    172     194   3.000   70.0 GUCGUGCUCCUGGCAGGCGdTdT CGCCUGCCAGGAGCACGACdTdT
    443     465   3.000   35.0 AUGCCAACUCUUAAGUCUUdTdT AAGACUUAAGAGUUGGCAUdTdT
    456     478   3.000   35.0 AGUCUUUUGUAAUUCUGGCdTdT GCCAGAAUUACAAAAGACUdTdT
    468     490   3.000   30.0 UUCUGGCUUUCUCUAAUAAdTdT UUAUUAGAGAAAGCCAGAAdTdT
    484     506   3.000   30.0 UAAAAAAGCCACUUAGUUCdTdT GAACUAAGUGGCUUUUUUAdTdT
    108     130   2.000   60.0 GGAAACGGUCGCCCAGAUCdTdT GAUCUGGGCGACCGUUUCCdTdT
    135     157   2.000   60.0 UGUAGCCUCACUGGAGGGCdTdT GCCCUCCAGUGAGGCUACAdTdT
    139     161   2.000   60.0 GCCUCACUGGAGGGCAUUGdTdT CAAUGCCCUCCAGUGAGGCdTdT
    150     172   2.000   60.0 GGGCAUUGCCCCGGAAGAUdTdT AUCUUCCGGGGCAAUGCCCdTdT
    171     193   2.000   65.0 AGUCGUGCUCCUGGCAGGCdTdT GCCUGCCAGGAGCACGACUdTdT
    201     223   2.000   65.0 GGAUGAGGCCACUCUGGGCdTdT GCCCAGAGUGGCCUCAUCCdTdT
    204     226   2.000   65.0 UGAGGCCACUCUGGGCCAGdTdT CUGGCCCAGAGUGGCCUCAdTdT
    245     267   2.000   65.0 CCCUGGAAGUAGCAGGCCGdTdT CGGCCUGCUACUUCCAGGGdTdT
    256     278   2.000   65.0 GCAGGCCGCAUGCUUGGAGdTdT CUCCAAGCAUGCGGCCUGCdTdT
    285     307   2.000   65.0 UGGUUCCCUGGCCCGUGCUdTdT AGCACGGGCCAGGGAACCAdTdT
    338     360   2.000   35.0 AACAGGAGAAGAAGAAGAAdTdT UUCUUCUUCUUCUCCUGUUdTdT
    345     367   2.000   35.0 GAAGAAGAAGAAGAAGACAdTdT UGUCUUCUUCUUCUUCUUCdTdT
    486     508   2.000   35.0 AAAAAGCCACUUAGUUCAGdTdT CUGAACUAAGUGGCUUUUUdTdT

#---------------------------------------
#---------------------------------------

#---------------------------------------
# Total_sequences: 1
# Total_hitcount: 85
#---------------------------------------

  File: hsfau.fasta

>HSFAU_308 %GC 50.0 Score 9 H.sapiens fau mRNA
aaaagtgagaggtcagactccta
>HSFAU_309 %GC 50.0 Score 9 H.sapiens fau mRNA
aaagtgagaggtcagactcctaa
>HSFAU_310 %GC 50.0 Score 9 H.sapiens fau mRNA
aagtgagaggtcagactcctaag
>HSFAU_351 %GC 50.0 Score 9 H.sapiens fau mRNA
aagaagaagaagacaggtcgggc
>HSFAU_166 %GC 55.0 Score 8 H.sapiens fau mRNA
aagatcaagtcgtgctcctggca
>HSFAU_279 %GC 55.0 Score 8 H.sapiens fau mRNA
aaagttcatggttccctggcccg
>HSFAU_330 %GC 55.0 Score 8 H.sapiens fau mRNA
aaggtggccaaacaggagaagaa
>HSFAU_354 %GC 55.0 Score 8 H.sapiens fau mRNA
aagaagaagacaggtcgggctaa
>HSFAU_357 %GC 55.0 Score 8 H.sapiens fau mRNA
aagaagacaggtcgggctaagcg
>HSFAU_393 %GC 55.0 Score 8 H.sapiens fau mRNA
aaccggcgctttgtcaacgttgt
>HSFAU_253 %GC 60.0 Score 7 H.sapiens fau mRNA
aagtagcaggccgcatgcttgga
>HSFAU_280 %GC 60.0 Score 7 H.sapiens fau mRNA
aagttcatggttccctggcccgt
>HSFAU_339 %GC 40.0 Score 7 H.sapiens fau mRNA
aaacaggagaagaagaagaagaa
>HSFAU_340 %GC 40.0 Score 7 H.sapiens fau mRNA
aacaggagaagaagaagaagaag