extractfeat.usage

emboss的linux版本的源代码

<b>Here is a sample session with extractfeat</b>
<p>
To write out the exons of a sequence:  
<p>

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

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

>HSFAU1_408_504 [exon] H.sapiens fau 1 gene
cagtgacgtgacacgcagcccacggtctgtactgacgcgccctcgcttcttcctctttct
cgactccatcttcgcggtagctgggaccgccgttcag
>HSFAU1_774_856 [exon] H.sapiens fau 1 gene
tcgccaatatgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggcc
aggaaacggtcgcccagatcaag
>HSFAU1_951_1095 [exon] H.sapiens fau 1 gene
gctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctggcaggc
gcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgactaccctg
gaagtagcaggccgcatgcttggag
>HSFAU1_1557_1612 [exon] H.sapiens fau 1 gene
gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag
>HSFAU1_1787_1912 [exon] H.sapiens fau 1 gene
gtggccaaacaggagaagaagaagaagaagacaggtcgggctaagcggcggatgcagtac
aaccggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgccaac
tcttaa

</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><p>
<p>
<b>Example 2</b>
<p>
To write out the exons with 10 extra bases at the start and end so that you can inspect the splice sites: 
<p>

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

% <b>extractfeat tembl:hsfau1 -type exon -before 10 -after 10 stdout </b>
Extract features from a sequence

>HSFAU1_408_504 [exon] H.sapiens fau 1 gene
ggtcgctcagcagtgacgtgacacgcagcccacggtctgtactgacgcgccctcgcttct
tcctctttctcgactccatcttcgcggtagctgggaccgccgttcaggtaagaatgg
>HSFAU1_774_856 [exon] H.sapiens fau 1 gene
ctttactcagtcgccaatatgcagctctttgtccgcgcccaggagctacacaccttcgag
gtgaccggccaggaaacggtcgcccagatcaaggtaaggctgc
>HSFAU1_951_1095 [exon] H.sapiens fau 1 gene
ttccctgtaggctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgct
cctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggaggccct
gactaccctggaagtagcaggccgcatgcttggaggtgagtgaga
>HSFAU1_1557_1612 [exon] H.sapiens fau 1 gene
cccactacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagact
cctaaggtgagtgaga
>HSFAU1_1787_1912 [exon] H.sapiens fau 1 gene
ccttctccaggtggccaaacaggagaagaagaagaagaagacaggtcgggctaagcggcg
gatgcagtacaaccggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccc
caatgccaactcttaagtcttttgta

</pre></td></tr></table><p>
<p>
<p>
<p>
<b>Example 3</b>
<p>
To write out the 10 bases around the start of all 'exon' features in the tembl database:  
<p>

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

% <b>extractfeat tembl:*  -type exon -before 5 -after -5 stdout </b>
Extract features from a sequence

>HSFAU1_408_504 [exon] H.sapiens fau 1 gene
ctcagcagtg
>HSFAU1_774_856 [exon] H.sapiens fau 1 gene
ctcagtcgcc
>HSFAU1_951_1095 [exon] H.sapiens fau 1 gene
tgtaggctca
>HSFAU1_1557_1612 [exon] H.sapiens fau 1 gene
tacaggtaaa
>HSFAU1_1787_1912 [exon] H.sapiens fau 1 gene
tccaggtggc
>HSFOS_889_1029 [exon] Human fos proto-oncogene (c-fos), complete cds.
ccacgatgat
>HSFOS_1783_2034 [exon] Human fos proto-oncogene (c-fos), complete cds.
tctaggactt
>HSFOS_2466_2573 [exon] Human fos proto-oncogene (c-fos), complete cds.
tctagttatc
>HSFOS_2688_3329 [exon] Human fos proto-oncogene (c-fos), complete cds.
tacaggagac
>HSTS1_1001_1205 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7, complete cds.
gcgccatgcc
>HSTS1_2895_2968 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7, complete cds.
ttcagatgaa
>HSTS1_5396_5570 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7, complete cds.
tccagggatc
>HSTS1_11843_11944 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7, complete cds.
tacagattat
>HSTS1_13449_13624 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7, complete cds.
ctcagatctt
>HSTS1_14133_14204 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7, complete cds.
tatagccagg
>HSTS1_15613_15750 [exon] Homo sapiens gene for thymidylate synthase, exons 1, 2, 3, 4, 5, 6, 7, complete cds.
tttagcttca
>AB009062_75_503 [exon] Homo sapiens HERG gene, exon 6.
tgcaggtcct
>HSFERG2_50_196 [exon] Human apoferritin H gene exons 2-4
ttcagtctta
>HSFERG2_453_578 [exon] Human apoferritin H gene exons 2-4
ttcagaaacc
>HSFERG2_674_999 [exon] Human apoferritin H gene exons 2-4
tgcagttgtg
>AP000504_13_134 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcactgtga
>AP000504_868_930 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
gataccaaaa
>AP000504_1081_1161 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cttaccaagc
>AP000504_2752_2875 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cccacctctc
>AP000504_3425_3584 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
gagacctcgg
>AP000504_3818_4038 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
gttacccttt
>AP000504_7507_7763 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ccagcccggg
>AP000504_9766_9875 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ttcaggctgg
>AP000504_10068_10193 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tccaggcgga
>AP000504_10357_10463 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ttcaggtacc
>AP000504_11631_11812 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cacagatctg
>AP000504_13026_13434 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaggtggt
>AP000504_14850_15164 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
gagggggagt
>AP000504_15284_15383 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctaaggtcga
>AP000504_15505_15578 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaggccgg
>AP000504_15737_15856 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cctaggactt
>AP000504_16337_16486 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tctaggcaat
>AP000504_16676_16987 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgcaggcact
>AP000504_18955_19059 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tcccttcaaa
>AP000504_19185_19264 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cttaccggtt
>AP000504_19402_19442 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcaccaaat
>AP000504_19797_19887 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcacctgtg
>AP000504_20043_20390 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cctaccatgg
>AP000504_20585_20645 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cttaccccca
>AP000504_22296_22401 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
atccttgaaa
>AP000504_23826_23936 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cccagctgac
>AP000504_24719_25381 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cctaggtaag
>AP000504_26111_26448 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
gctgtagagt
>AP000504_28403_28525 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcacggttt
>AP000504_28617_28671 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cttacccaag
>AP000504_30215_30266 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tggccatggg
>AP000504_31238_31363 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
aacaggtctc
>AP000504_31486_31691 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctgagtgaaa
>AP000504_33605_33675 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
gttcctcacc
>AP000504_33846_34001 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcacctctg
>AP000504_35893_36156 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tttacctgcc
>AP000504_36240_36569 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ctcacctttg
>AP000504_37069_37123 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cttacctgca
>AP000504_40724_40877 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ggaagagcag
>AP000504_41897_41953 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
ggcaggatac
>AP000504_42687_42753 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
tgcaggcttc
>AP000504_42999_43085 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.
cccaggttac
>AP000504_46996_47081 [exon] Homo sapiens genomic DNA, chromosome 6p21.3, HLA Class I region, section 3/20.