NemaFootPrinter: a web based software for the identification of conserved non-coding genome sequence regions between C. elegans

Background: NemaFootPrinter (Nematode Transcription Factor Scan Through Philogenetic Footprinting) is a web-based software for interactive identification of conserved, non-exonic DNA segments in the genomes of C. elegans and C. briggsae. It has been implemented according to the following project specifications: a) Automated identification of orthologous gene pairs. b) Interactive selection of the boundaries of the genes to be compared. c) Pairwise sequence comparison with a range of different methods. d) Identification of putative transcription factor binding sites on conserved, non-exonic DNA segments. Results: Starting from a C. elegans or C. briggsae gene name or identifier, the software identifies the putative ortholog (if any), based on information derived from public nematode genome annotation databases. The investigator can then retrieve the genome DNA sequences of the two orthologous genes; visualize graphically the genes' intron/exon structure and the surrounding DNA reg...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Davide Rambaldi, Alessandro Guffanti, Paolo Morandi, Giuseppe Cassata
• Keywords: BMCBI 2005, Genome Annotation Databases, Non-exonic Dna Segments, Transcription Factor