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

Abstract

BackgroundNemaFootPrinter (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.ResultsStarting 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 regions; select, through an interactive graphical user interface, subsequences of the two gene regions. Using a bioinformatics toolbox (Blast2seq, Dotmatcher, Ssearch and connection to the rVista database) the investigator is able at the end of the procedure to identify and analyze significant sequences similarities, detecting the presence of transcription factor binding sites corresponding to the conserved segments. The software automatically masks exons.DiscussionThis software is intended as a practical and intuitive tool for the researchers interested in the identification of non-exonic conserved sequence segments between C. elegans and C. briggsae. These sequences may contain regulatory transcriptional elements since they are conserved between two related, but rapidly evolving genomes. This software also highlights the power of genome annotation databases when they are conceived as an open resource and the possibilities offered by seamless integration of different web services via the http protocol.Availability: the program is freely available at

Phylogenetic simulation of promoter evolution: estimation and modeling of binding site turnover events and assessment of their impact on alignment tools

“…Many excellent alignment tools were not evaluated because: they did not meet one of the above criteria; their algorithms were similar to one of five tools we selected; and/or they did not show a significantly different performance in other evaluations. For example, ACANA [ 21 ], BLASTZ [ 76 ], MUMmer [ 77 ], and SSEARCH [ 78 ] were not selected because of the first criterion, and T-COFFEE [ 22 ], POA [ 79 ] and MAFFT [ 80 ] were not evaluated due to the second criterion. Our study is therefore not considered to be a systematic evaluation of all available good alignment tools and rather as a representative but somewhat subjective cross-section.…”

Using Web Services for Linking Genomic Data to Medical Information Systems

“…Other projects likeN emaFootPrinter [13] or the Centerfor Biological Sequence Analysis' (CBS) Genome Atlas Database [14] applyW eb servicest oa ccess genome annotation databases. At the EBI [15] many resources area ccessibleb ym eanso fW eb services.Theservicesoffer diversepossibilitiesfor the useofanalysistools, homology searches, multiple alignment, structural analysis, text mining or data retrieval.…”

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society

“…Rambaldi et al . [8] developed NemaFootPrinter (Nematode Transcription Factor Scan Through Phylogenetic Footprinting), a web-based software for interactive identification of conserved, non-exonic DNA segments in their genomes. This software relies on the identification of orthologous genes and on the manual selection of gene boundaries.…”