[BiO BB] Query
Jaya Handa
rtanishya at gmail.com
Tue Dec 2 01:14:57 EST 2008
Hello Sir
I wish to know when we read bacterial genomes in ncbi how do you number.
Suppose the + starand is 5'-3' and - strand is 3'-5'.
now if we number + trand as [5'] 1,2,3,4 [3'] bases then will the - strand
be like [3'] 4,3,2,1 [5'].
Suppose we read this
source 1..2256640
/organism="Bifidobacterium longum NCC2705"
/mol_type="genomic DNA"
/strain="NCC2705"
/db_xref="taxon:206672
<http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=206672>"
gene <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=58012118&from=49&to=288&view=gbwithparts>
49..288
/gene="cspA"
/locus_tag="BL0001"
CDS <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=58012118&from=49&to=288&view=gbwithparts>
49..288
/gene="cspA"
/locus_tag="BL0001"
/note="CspA; COG family: cold shock proteins; PFAM_ID:
CSD"
/codon_start=1
/transl_table=11
<http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG11>
/product="cold shock protein"
/protein_id="AAN23868.1
<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=AAN23868.1>"
/db_xref="GI:23325186"
gene <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=58012118&from=526&to=2151&view=gbwithparts>
526..2151
/gene="groEL"
/locus_tag="BL0002"
CDS <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=58012118&from=526&to=2151&view=gbwithparts>
526..2151
/gene="groEL"
/locus_tag="BL0002"
/note="GroEL; COG family: chaperonin GroEL (Hsp60 family);
PFAM_ID: cpn60_TCP1"
/codon_start=1
/transl_table=11
<http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG11>
/product="chaperone"
/protein_id="AAN23869.1
<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=AAN23869.1>"
/db_xref="GI:23325187"
gene <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=58012118&from=2248&to=2538&view=gbwithparts>
complement(2248..2538)
/locus_tag="BL0003"
CDS <http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=58012118&from=2248&to=2538&view=gbwithparts>
complement(2248..2538)
/locus_tag="BL0003"
/note="COG family: methyl-accepting chemotaxis protein"
/codon_start=1
/transl_table=11
<http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c#SG11>
/product="hypothetical protein"
/protein_id="AAN23870.1
<http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=AAN23870.1>"
/db_xref="GI:23325188"
Now the complement will be read as continuation of 2151 then we read same
for both +/- strand irrespective of its orientation.
Please clarify me on this
Thank You and waiting for your reply
Jaya Handa
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