[EMBOSS] getorf question..

[Ted Chiang]

Hi,

I'm using getorf as follows:

$ getorf sequence.fasta -find 1 -noreverse -minsize 100

Among the results one of the ORFs I get is:

MMSNSSSEIDVQEPNIVSDASCNTEEQLKTVDDVLIHCQVIYDALQNLDKKIDVIRRKVS
KIQRFHARSLWTNHKRYGYKKHSYRLVKKLKLQKMKKNEVYETFSYPESYSPTLPVSRRE
NNSPSNLPRPSFCMEEYQRAELEEDPILSRTPSPVHPSDFSEHNCQPYYASDGATYGSSS
GLCLGNPRADSIHNTYSTDHASAAPPSVTRSPVENDGYIEEGSITKHPSTWSVEAVVLFL
KQTDPLALCPLVDLFRSHEIDGKALLLLTSDVLLKHLGVKLGTAVKLCYYIDRLKQGKCF
EN


However, it does not give me a smaller ORF that begins with the marked '^'
below:

MMSNSSSEIDVQEPNIVSDASCNTEEQLKTVDDVLIHCQVIYDALQNLDKKIDVIRRKVS
KIQRFHARSLWTNHKRYGYKKHSYRLVKKLKLQKMKKNEVYETFSYPESYSPTLPVSRRE
                                  ^
NNSPSNLPRPSFCMEEYQRAELEEDPILSRTPSPVHPSDFSEHNCQPYYASDGATYGSSS
GLCLGNPRADSIHNTYSTDHASAAPPSVTRSPVENDGYIEEGSITKHPSTWSVEAVVLFL
KQTDPLALCPLVDLFRSHEIDGKALLLLTSDVLLKHLGVKLGTAVKLCYYIDRLKQGKCF
EN


Is there a bug or am I missing something?   The DNA input sequence is:


>sequence.fasta
ggtgtcgcgggagctctctgatccactcaggggtcagggcatcactggtctcgcgtgcgc
gtgaccaggcccggtttccggtgccaggacctttccgaagcgtcgagtggcctaacggtc
acagctgtcgcccatcggagaggcaggactactgcgagcagttttaccgcgacctccgga
ggccggcgtgacaggctctgtcactaaaataggagtagaggtttaccactcttaggtgac
taagcagtatcacaaataaaccctccagcaagtttaaaaataattaggtccaactcagag
gaagtggagtttctcctgttgcacaaaaatgatgtctaacagctccagtgaaatcgatgt
gcaggaaccgaatattgtatctgacgcatcctgtaatactgaagagcaactgaagacagt
tgatgatgtccttattcattgccaggttatatatgatgctctgcaaaacctggataagaa
gattgatgtgattcgtagaaaggtttcaaaaatccaacgtttccatgcgagatccctgtg
gacaaatcataagcgatatggatataaaaagcattcttaccggcttgttaaaaagcttaa
actccagaaaatgaagaaaaatgaggtttacgagacattctcctaccctgaaagttacag
ccccactttaccagtgtcaaggcgtgagaataattccccgagcaaccttccaaggccatc
cttttgcatggaagaataccagcgagctgagctggaggaggacccgatcctcagccgcac
tccgagtccagtgcatccctcagatttctctgagcataattgtcagccgtattatgcatc
tgatggtgcaacgtatggttcttcttcagggctctgccttggcaaccctcgggctgacag
catccacaacacttactcaactgaccatgcttctgcagcaccaccttcagttacaaggtc
accagttgaaaatgacggttacatagaggaaggaagcatcactaagcacccttcaacctg
gtcggtggaagcagtggtcctatttctaaaacaaacagatcctcttgcattatgccctct
tgtcgacctcttcagaagccatgaaattgacgggaaggctctgctcctactcacgagtga
cgtgttgctgaagcacttgggggtgaagctgggaacggctgtgaagctatgctactacat
tgaccgacttaaacaaggaaaatgctttgaaaattgaaaaaatccttgtgcaaatttaga
ttgggccaacttctagaggcaccaatgccttcttagtgtggaatcatttttctgcccttt
agtcgtttttgttttgtagaaagtatctctcaaaatatattatagctagaattgtagaac
tatgttatagtccagtctacttctttaaaaaccatttaaactgctagatagtattagaat
agtccaatagaaaattcattctttataggtctttaaaaattacttttattatattgttta
caaatatatttcatgcaagaaacagaaaaaaaaaaaaccctttgattctggttcatctcg
atacagagaaccaaaacagctaagagaggtattatcagggttgacaactcctatgattga
atctatgggaattattcctcagaagagaatttaaaggtgtacccatatatatctctttct
ggagtattttatctgtctgatgttgcagtattctacaagtttccagaaagagaatagcca
tataaattattttcctttctgctattatttctctatatgttttatttattcagatttaga
gtaaaaaataagcatataaacttttattatgtgctcttaacagttttaagataaactata
ggatagatagaatggttattttatgcaagaaatattgtaccgcaagggtggtttggatga
agtctgactactttttttcaaacaaactattatattaaaactgtcatattttggctaagt
ttggacctataactacactttcattgtttgcatctctctatgaagatacgtctgtccaaa
cttttaaaaggcataactgtattttatgtgtttattctttatatagatagtattttatat
tttattctcacccgaagtattcacacaatctttttaaaaaaaatttgaaatggcattttg
tattgccacagaggtaggatgagccatatattagtgaaatgttttattttgtaaaatata
aatggattatttgccatcattagtacctctcaacttactttttagaggacaagaaacaat
ctgtagattggtttccatacagggaagttctccgtcctatgcaatgtttctaattaattt
gcttaattctgagccattaatcctgctacactttgaatgatacattaattcagactaatc
tttgggggctttattttgtaagttagaactttcaagggaaacatgttcaacactattatt
ttgttataaatttataactttgttattacattgtgtaacaaatataaggtttacgagcta
tgagaattggtgctatcaccattagctatttgctgtaatgtcaagaaaatgttcaccaga
tgcaagaatgtaccttttctttttagaaagccaaatgtactttagacatgaatgcaacta
tttaaagaatagcttcatcaatgttattccttacatgtcataagattcttacttaaactt
ggtcttctttcaaattgtttgtatgaagatgctgtacccacttgaacagtcctcaggtgt
ttacataaatactatgttttacagttttcatattttaaaatattaataaagttaaatcac
aatagttcaaaaaaaaaaaaaaaa


-Ted

===================================
Ted Chiang, Analyst
Centre for Computational Biology 
Hospital for Sick Children, Toronto
t: 416.813.7028
e: tchiang at sickkids.ca
===================================