FastER: Identification of genes with fast-evolving regions in closely related genomes

Yu Zheng, Rich Roberts & Simon Kasif

Bioinformatics Graduate Program, Boston University

Introduction:

FastER is a software for identifying orthologous gene pairs that appear to have fast-evolving regions between two closely related genomes. Its input can be either two closely related whole genome sequences or two closely related orthologous sequences. It consists of two steps: first, it will detect all regions with overrepresented nonsynonymous mutations; second, it will test the nonsynonymous evolution rate against the neutral evolution rate in that gene. The full system IS Described in the paper(link).

Supplementary data to the paper:

  1. Gene list from Neiseria meningitidis strain MC58 and Z2491(list)
  2. Gene list from Streptococcus pneumoniae TIGR4 and R6 (list)
  3. Gene list from Mycobacterium tuberculosis CDC1551 and HR37v (tab delimited:gene_id_1 gene_name_1 gene_id_2 gene_name_2 function) (list)
  4. Gene list from Escherichia coli K12 and O157:H7 (list)
  5. Gene list from Escherichia coli K12 and CFT073 (list)
  6. Gene list from Escherichia coli O157:H7 and CFT073 (list)

Software download and usage:

You can download Faster v1.0(updated 7/29/05) and run it. A set of preinstalled PERL packages are necessary. Download clustalW.

Please address questions on installation to: zhengyu@alum.bu.edu

Copyright©Yu Zheng 2004