[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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