Number Of Gene Cluster From Blast Output

Question

[armahmud3]

After parsing genbank file and blast output(xml file) using biopython library, how can I calculate the number of linked gene cluster at different stringent level (0 to 100) increment of 10. Example

0 (stringent level),13456 (number of gene cluster) 10,234 20,234 30,200 40,190 50,187 60,187 70,100 80,95 90,55 100,45

[Manu Prestat]

BLAST is not a "sensu stricto" clustering tool but a pairwise aligner, so: how do you define a cluster in your case ? Something generated with OrthoMCL or BlastClust ?

[armahmud3]

I define it as homologous gene groups.

Answer 1

[Pierre]

Not sure if I understand your question correctly, however, in case that you want to cluster / group your sequences based on pairwise sequence similarity, then you can use blastclust (already includede in blast+ package) to do this.

[armahmud3]

Thank you pierre. I, actually need the python script.

[Pierre]

In principle, blastclust would give you clusters of homologous sequences (presumably paralogs). You just need to have a fasta file containing all sequences that you'd like to have as clustered.