Translating Reading Frames
Given a sequence of DNA, it is necessary to examine all six
reading frames of the DNA to find the coding regions the cell uses
to make proteins.
Very often we won't know where, in the DNA we are studying, the
cell begins translating DNA into protein. Since we don't know where
the translation begins, we have to consider the six possible reading
frames when looking for coding regions.
Your task is to write a program to translate a DNA sequence,
given in a GenBank file format called sequences.gb, into all six
reading frames as output.
Here is the input file:
LOCUS FJ529397 894 bp mRNA linear VRL 15-APR-2009
DEFINITION Human rotavirus A isolate RUS-Nov04-H390 outer capsid protein VP4
(VP4) mRNA, partial cds.
ACCESSION FJ529397
VERSION FJ529397.2 GI:226739224
KEYWORDS .
SOURCE Human rotavirus A
ORGANISM Human rotavirus A
Viruses; dsRNA viruses; Reoviridae; Rotavirus; Rotavirus A.
REFERENCE 1 (bases 1 to 894)
AUTHORS Zhirakovskaya,E., Tikunov,A. and Tikunova,N.
TITLE Sequence analysis of VP4 and VP7 genes from human rotaviruses
isolated in Western Siberia, Russia
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 894)
AUTHORS Zhirakovskaya,E., Bodnev,S., Kachko,A. and Tikunova,N.
TITLE Direct Submission
JOURNAL Submitted (06-DEC-2008) Russian Federation Ministry of Health and
Social Development, State Research Center of Virology and
Biotechnology 'Vector', Koltsovo, Novosibirsk region 630559, Russia
REFERENCE 3 (bases 1 to 894)
AUTHORS Zhirakovskaya,E., Tikunov,A. and Tikunova,N.
TITLE Direct Submission
JOURNAL Submitted (14-APR-2009) Siberian Branch of Russian Academy of
Sciences, Institute of Chemical Biology and Fundamental Medicine,
Lavrentiev Ave. 8, Novosibirsk 630090, Russia
REMARK Sequence update by submitter
COMMENT On Apr 14, 2009 this sequence version replaced gi:220061711.
FEATURES Location/Qualifiers
source 1..894
/organism="Human rotavirus A"
/mol_type="mRNA"
/isolate="RUS-Nov04-H390"
/isolation_source="stool specimen of an 11 month old male
with diarrhea"
/host="Homo sapiens"
/db_xref="taxon:10941"
/segment="4"
/country="Russia: Novosibirsk"
/collection_date="Mar-2004"
/note="genotype: P[4]G1"
gene 1..>894
/gene="VP4"
CDS 7..>894
/gene="VP4"
/codon_start=1
/product="outer capsid protein VP4"
/protein_id="ACL79516.2"
/db_xref="GI:226739225"
/translation="MASLIYRQLLTNSYSVDLHDEIEQIG…
YAPVNWGHGEINDSTTVEPVLDGPYQPTTFKPPNDYWLLI…
TAVIAVEPHVSQTNRQYVLFGENKQFNLENSSDKWKFFEM…
NRLVGMLKYGGRVWTFHGETPRATTDSSNTADLNNISIII…
INNGLPPIQNTRNVVPLSLSSRSIQYRRAQVNEDITISKT…
GNSVIKLGGLGYKWSEISYK"
ORIGIN
1 tataaaatgg cttcgctcat ttatagacaa cttctcacta attcatattc ggtagacttg
61 catgacgaaa tagaacagat tggatcggag aaaactcaaa atgtgacggt aaatccaggc
121 ccatttgcac agactagata cgctccagtt aattggggac acggagagat taatgattca
181 actacagtgg aaccagtttt agatggtcct tatcaaccaa ctacattcaa accacccaat
241 gattattggc tgcttattag ttcaaataca gatggagtag tctatgagag tacaaataat
301 agtgactttt ggacagcagt tatcgctgtt gaaccacatg tcagtcaaac aaataggcaa
361 tatgttttat ttggtgaaaa taagcagttt aacttagaaa atagttcaga taaatggaaa
421 tttttcgaaa tgtttaaagg tagtagtcag agtgattttt ctaatagacg gactttaacc
481 tctaataata gacttgtagg aatgctaaaa tatggtggaa gagtatggac atttcatggt
541 gaaacaccaa gagctactac tgatagttcg aatactgcgg atttaaataa tatatcaatt
601 ataattcatt cagagtttta tattattcca agatcccaag aatctaaatg taatgaatat
661 attaataatg gtttaccacc aattcaaaat actagaaatg tagttccatt atctctatca
721 tccagatcta ttcaatatag aagagcacaa gttaatgaag atattacaat ttcaaaaact
781 tcattatgga aagaaatgca atataataga gatattataa taagatttaa atttggtaat
841 agtgtcataa aattaggagg attgggttat aaatggtcag aaatatcata caaa
//
Output should be to the screen in the form of "Reading Frame n"
where n is a number betwee 1 and 6 inclusive followed by the
translation of the given reading frame.
Given a sequence of DNA, it is necessary to examine all six
reading frames of the DNA to find the coding regions the cell uses
to make proteins.
Very often we won't know where, in the DNA we are studying, the
cell begins translating DNA into protein. Since we don't know where
the translation begins, we have to consider the six possible reading
frames when looking for coding regions.
Your task is to write a program to translate a DNA sequence,
given in a GenBank file format called sequences.gb, into all six
reading frames as output.
Here is the input file:
LOCUS FJ529397 894 bp mRNA linear VRL 15-APR-2009
DEFINITION Human rotavirus A isolate RUS-Nov04-H390 outer capsid protein VP4
(VP4) mRNA, partial cds.
ACCESSION FJ529397
VERSION FJ529397.2 GI:226739224
KEYWORDS .
SOURCE Human rotavirus A
ORGANISM Human rotavirus A
Viruses; dsRNA viruses; Reoviridae; Rotavirus; Rotavirus A.
REFERENCE 1 (bases 1 to 894)
AUTHORS Zhirakovskaya,E., Tikunov,A. and Tikunova,N.
TITLE Sequence analysis of VP4 and VP7 genes from human rotaviruses
isolated in Western Siberia, Russia
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 894)
AUTHORS Zhirakovskaya,E., Bodnev,S., Kachko,A. and Tikunova,N.
TITLE Direct Submission
JOURNAL Submitted (06-DEC-2008) Russian Federation Ministry of Health and
Social Development, State Research Center of Virology and
Biotechnology 'Vector', Koltsovo, Novosibirsk region 630559, Russia
REFERENCE 3 (bases 1 to 894)
AUTHORS Zhirakovskaya,E., Tikunov,A. and Tikunova,N.
TITLE Direct Submission
JOURNAL Submitted (14-APR-2009) Siberian Branch of Russian Academy of
Sciences, Institute of Chemical Biology and Fundamental Medicine,
Lavrentiev Ave. 8, Novosibirsk 630090, Russia
REMARK Sequence update by submitter
COMMENT On Apr 14, 2009 this sequence version replaced gi:220061711.
FEATURES Location/Qualifiers
source 1..894
/organism="Human rotavirus A"
/mol_type="mRNA"
/isolate="RUS-Nov04-H390"
/isolation_source="stool specimen of an 11 month old male
with diarrhea"
/host="Homo sapiens"
/db_xref="taxon:10941"
/segment="4"
/country="Russia: Novosibirsk"
/collection_date="Mar-2004"
/note="genotype: P[4]G1"
gene 1..>894
/gene="VP4"
CDS 7..>894
/gene="VP4"
/codon_start=1
/product="outer capsid protein VP4"
/protein_id="ACL79516.2"
/db_xref="GI:226739225"
/translation="MASLIYRQLLTNSYSVDLHDEIEQIG…
YAPVNWGHGEINDSTTVEPVLDGPYQPTTFKPPNDYWLLI…
TAVIAVEPHVSQTNRQYVLFGENKQFNLENSSDKWKFFEM…
NRLVGMLKYGGRVWTFHGETPRATTDSSNTADLNNISIII…
INNGLPPIQNTRNVVPLSLSSRSIQYRRAQVNEDITISKT…
GNSVIKLGGLGYKWSEISYK"
ORIGIN
1 tataaaatgg cttcgctcat ttatagacaa cttctcacta attcatattc ggtagacttg
61 catgacgaaa tagaacagat tggatcggag aaaactcaaa atgtgacggt aaatccaggc
121 ccatttgcac agactagata cgctccagtt aattggggac acggagagat taatgattca
181 actacagtgg aaccagtttt agatggtcct tatcaaccaa ctacattcaa accacccaat
241 gattattggc tgcttattag ttcaaataca gatggagtag tctatgagag tacaaataat
301 agtgactttt ggacagcagt tatcgctgtt gaaccacatg tcagtcaaac aaataggcaa
361 tatgttttat ttggtgaaaa taagcagttt aacttagaaa atagttcaga taaatggaaa
421 tttttcgaaa tgtttaaagg tagtagtcag agtgattttt ctaatagacg gactttaacc
481 tctaataata gacttgtagg aatgctaaaa tatggtggaa gagtatggac atttcatggt
541 gaaacaccaa gagctactac tgatagttcg aatactgcgg atttaaataa tatatcaatt
601 ataattcatt cagagtttta tattattcca agatcccaag aatctaaatg taatgaatat
661 attaataatg gtttaccacc aattcaaaat actagaaatg tagttccatt atctctatca
721 tccagatcta ttcaatatag aagagcacaa gttaatgaag atattacaat ttcaaaaact
781 tcattatgga aagaaatgca atataataga gatattataa taagatttaa atttggtaat
841 agtgtcataa aattaggagg attgggttat aaatggtcag aaatatcata caaa
//
Output should be to the screen in the form of "Reading Frame n"
where n is a number betwee 1 and 6 inclusive followed by the
translation of the given reading frame.