Visualize & cluster one-mode projection of a bi-partite graph


A lot of genomic knowledge are often curated in the form of genesets where a combination of genes are involved in certain biological process/function/pathway. In other words, a pathway is often enriched with different combination of genes. Similarly this can also be related to patient-genesets data structure. This can be thought of as a bipartite…

Genetic Ancestry of Nepalis


One evening, few years back, my grandpa passed down a legacy to me and my cousins – the story of our ancestors. I belong to a Newar community which is one among the indigenous people of Kathmandu Valley. Newars have been living in Kathmandu valley from the prehistoric times. As per my grandpa, our ancestors…

Bioinformatics for personal genome interpretation


Following paper is a very good review on the the current bioinformatics methods applied in Personalize Genomics and the challenges to understand the biological data. Capriotti E, Nehrt NL, Kann MG, Bromberg Y. Bioinformatics for personal genome interpretation.Brief Bioinform. 2012 Jan 13. Abstract: An international consortium released the first draft sequence of the human genome…

Download Sequence from Accession Number using Perl


If you are looking to download batch of sequences from public database such as Genbank using the accession number, the following perl script that I’ve written may be quite handy. This script uses a BioPerl module “Bio::DB::GenBank“. All the accession number must be present within the file accnumber.txt each separated my a comma. And also,…