IGS Browser 
                    
        

General features of IGS
There are 2458 IGS in E. coli in K12 MG1655. The IGS were assigned an identification number from 1 to 2458 starting from ‘ori’ on the + strand.
The length and GC% of each IG was computed using Microsoft Office Excel 2003. The orientation, proximal gene and distal gene information of IGS provided by EcoGene was confirmed by manual curation – by comparison with the E. coli genome map obtained from EcoCyc and corrections were made where required. The position of IGS whether between genes in an operon or between operons was manually determined from the genome map.
The genomic coordinates of the sequences were determined using the standalone blast tool by performing a megablast of the IGS against the genome of E. coli K12 from GenBank.
The IGS ranged in length from 47 to 1231 bp; their %GC content ranged between 19 – 68 %. About 30% of IGS had a GC content >50%. The IGS were categorized based on different parameters as listed below.

IGS categorized based on length
47-200 bp    1684
201-400 bp    617
401-600 bp    123
601-800 bp    26
800-1000 bp    6
1001-1231 bp    2

IGS categorized based on % GC
19-20    1
20-40    1025
40-60    1418
60-68    14

IGS categorized based on orientation
Codirectional+    764
Codirectional-    739
Divergent    732
Convergent    223

IGS categorized based on position
Between operons    2142
Between genes    316

IGS categorized based on sequence and structural simialrity
Showing sequence similarity    462
Showing structural similarity    390
Showing no similarity    1641


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© Sathi Ravi Kanth Reddy, 2012