extractfeat.usage

emboss的linux版本的源代码

accaggcatt
>AP000504_50596_50669 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgcagaggca
>AP000504_50879_51001 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaggaagg
>AP000504_52110_52224 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cacagctacc
>AP000504_52348_52449 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcagtgtaa
>AP000504_53426_53489 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cctaggtgat
>AP000504_53901_53950 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tacagctgga
>AP000504_54324_54447 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgcagggggt
>AP000504_54909_55013 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
accagccacg
>AP000504_55242_55305 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tctagggggc
>AP000504_55723_55779 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgaagatacc
>AP000504_55925_55987 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cccagggttc
>AP000504_56128_56204 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cgtaggtatc
>AP000504_56288_56386 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
accagcctca
>AP000504_56484_56530 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgcaggggag
>AP000504_56733_57055 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaggctcg
>AP000504_59988_60040 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cagagatgca
>AP000504_63714_63775 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cacagcagcc
>AP000504_64760_64927 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tctaggtaag
>AP000504_66908_67344 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cccaggcagc
>AP000504_71741_72164 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
actgtggaat
>AP000504_72744_73649 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tttaccataa
>AP000504_73962_74192 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcatggcct
>AP000504_74520_74709 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cctacctggg
>AP000504_74856_74931 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaccaatg
>AP000504_75374_75489 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaccatct
>AP000504_76058_76160 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaccaggc
>AP000504_77125_77207 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcacttcac
>AP000504_77820_78148 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaccggct
>AP000504_79023_79187 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgattagaat
>AP000504_79451_80175 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
agcaggtctc
>AP000504_81318_81943 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgcaggtctc
>AP000504_83295_85730 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ggctccccaa
>AP000504_85819_85964 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
gagatgagga
>AP000504_86305_86403 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cttaccttga
>AP000504_86550_86648 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcactgtag
>AP000504_86730_86803 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ccaaccttca
>AP000504_87402_87556 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcacatgcg
>AP000504_87948_88090 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
catacctcct
>AP000504_91393_91628 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ccccgggcga
>AP000504_92264_92384 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tttagagacc
>AP000504_94413_94530 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ttcagatgaa
>AP000504_94645_94841 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgcagatgtt
>AP000504_95076_95129 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cccagagtga
>AP000504_95289_95363 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgtagagtga
>AP000504_96214_96449 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ttcagtgtcg
>AP000504_97518_97647 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cacagccatc
>AP000504_98437_98634 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cgcagcacga
>AP000504_98843_99095 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ttcagatcaa
>AP000504_99439_99516 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cccagattct
>AP000504_99847_99959 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cacaggacag
>AB000360_808_2266 [exon] Homo sapiens PIGC gene, complete cds.
cttttagtaa
>HSHBB_19289_19632 [exon] Human beta globin region on chromosome 11.
ggagccaaca
>HSHBB_19755_19977 [exon] Human beta globin region on chromosome 11.
catagactcc
>HSHBB_20833_21080 [exon] Human beta globin region on chromosome 11.
aacagctcct
>HSHBB_34478_34622 [exon] Human beta globin region on chromosome 11.
tccacacact
>HSHBB_34745_34967 [exon] Human beta globin region on chromosome 11.
cacaggctcc
>HSHBB_35854_36069 [exon] Human beta globin region on chromosome 11.
aacagctcct
>HSHBB_39414_39558 [exon] Human beta globin region on chromosome 11.
tccacacact
>HSHBB_39681_39903 [exon] Human beta globin region on chromosome 11.
cacaggctcc
>HSHBB_40770_40985 [exon] Human beta globin region on chromosome 11.
aacagctcct
>HSHBB_45710_45800 [exon] Human beta globin region on chromosome 11.
acactgtagt
>HSHBB_45922_46145 [exon] Human beta globin region on chromosome 11.
cacagtctcc
>HSHBB_46997_47124 [exon] Human beta globin region on chromosome 11.
cccagctctt
>HSHBB_54740_54881 [exon] Human beta globin region on chromosome 11.
tgcttacact
>HSHBB_55010_55232 [exon] Human beta globin region on chromosome 11.
ctcagattac
>HSHBB_56131_56389 [exon] Human beta globin region on chromosome 11.
cgcagctctt
>HSHBB_62137_62278 [exon] Human beta globin region on chromosome 11.
tgcttacatt
>HSHBB_62187_62278 [exon] Human beta globin region on chromosome 11.
acaccatggt
>HSHBB_62390_62408 [exon] Human beta globin region on chromosome 11.
attggtctat
>HSHBB_62409_62631 [exon] Human beta globin region on chromosome 11.
cttaggctgc
>HSHBB_63482_63742 [exon] Human beta globin region on chromosome 11.
cacagctcct
>GMGL01_363_460 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA detected).
gaaatatggg
>GMGL01_555_663 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA detected).
aataggatat
>GMGL01_2182_2286 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA detected).
tgtaggtgcg
>GMGL01_3065_3208 [exon] Glycine max leghemoglobin gene or pseudogene (no mRNA detected).
cgtaggtggt

</pre></td></tr></table><p>
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<p>
<b>Example 4</b>
<p>
To extract the CDS region with the exons joined into one sequence: 
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<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>extractfeat tembl:hsfau1 -type CDS -join stdout </b>
Extract features from a sequence

>HSFAU1_782_1912 [CDS] H.sapiens fau 1 gene
atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg
gtcgcccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtc
gtgctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggag
gccctgactaccctggaagtagcaggccgcatgcttggaggtaaagtccatggttccctg
gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
cccacctttggcaagaagaagggccccaatgccaactcttaa

</pre></td></tr></table><p>
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<p>
<p>
<b>Example 5</b>
<p>
To write out the 7 residues around all phosphorylated residues in the tsw database:  
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>extractfeat tsw:*  -type mod_res -value phosphorylation* -before 3 -after -4 stdout </b>
Extract features from a sequence

>OPSD_HUMAN_343_343 [mod_res] RHODOPSIN.
TETSQVA
>PAXI_HUMAN_118_118 [mod_res] PAXILLIN.
EHVYSFP

</pre></td></tr></table><p>
<p>
<a href="#input.5">Go to the input files for this example</a><br><p>