FEATURE EXPRESSIONS

[Fristensky, (1993) NAR 21:5997-6003]

GenBank flatfile entries specify the location of parts of the sequence in the Features Table

FEATURE TABLE: 

CDS             join(M38619:160..256,M38620:11..307,
                M38621:11..179,M38622:11..176,
                M38623:11..250,11..103)
                /product="green visual pigment"
                /gene="G101"
                /codon_start=1


RESULTANT SEQUENCE:

>ASYPIGG6:CDS1
atggccgcacacgagcctgtgttcgccgcccggcgccacaatgaagacac
cacaagggagtctgcatttgtctacacaaatgctaataatacaagag
atccttttgaaggaccaaactatcacattgcccctcgatgggtctacaac
gtatcatccttatggatgatctttgttgtcattgcatcagtcttcactaa
tggtttggtaattgtagcaacagcaaagttcaagaagctgcgacaccctc
taaactggattctggtaaacctggctatagccgatctcggggagacagtt
cttgccagcacaatcagtgtcatcaaccagatcttcggctacttcatcct
tggacacccaatgtgcgtttttgaggggtggacggtgtctgtctgtg
gtatcacagctctgtggtctctgactataatctcctgggagcgctgggtg
gttgtgtgcaagccatttggaaatgttaaattcgatggcaaatgggcagc
aggtggcatcatcttctcctgggtttgggccatcatctggtgcacccctc
caatctttggctggagcag
gtactggccccatggtctgaagacatcctgtggccctgatgtgttcagtg
gcagtgaggatccaggagtggcctcctacatgatcaccctaatgcttacc
tgctgtattcttcctctgtccatcattatcatttgctacatttttgtctg
gagtgccatccaccag
gtcgcccagcagcagaaagactcagagtccactcagaaggcagagaagga
agtgtccaggatggtggtagtgatgatccttgcctttattgtgtgctggg
gaccatatgcctcctttgccaccttctctgcagtgaacccaggttatgcc
tggcacccactggcagccgctatgcccgcttacttcgccaagagtgccac
catctacaatcccatcatttacgtcttcatgaaccgccag
ttccggagctgtatcatgcagctgtttggaaagaaggtggaggatgcatc
agaggtttccggctctaccacagaagtttctacagcctcgtaa

Feature expressions evaluate to sequences, in the same way that algebraic expressions evaluate to numbers. By creating expressions defining 5' untranscribed regions of genes, the sequences themselves can be extracted from the GenBank dataset.

Sample Feature Expression file:
Defense gene promoter regions

@AF002277:1..2088
@AF002278:1..1372
@AF017277:1..100
@AJ001627:1..690
@D10661:1..1493
@D10662:1..1889
@D76437:1..1354
@J03679:1..1520
@L77080:1..887
@M59196:1..379
@M63634:1..1646
@M83314:1..1337
@S68111:1..2051
@U11716:1..1432
@U31669:1..1123
@U48862:1..840
@U48863:1..1082
@U89895:1..964
etc......................