Abstract
UpCoT is a pipeline tool developed by automating the series of steps involved in prediction of cis-regulatory elements. UpCoT generates orthologs for each gene in target genome using bi-directional best blast hit against the reference genomes, then identifies potential orthologous transcriptional units using intergenic distance. Finally it generates the FASTA files containing upstream sequences of orthologous transcriptional units of each gene in target genome. The inputs of UpCoT are protein sequence files (*.faa), genome sequence files (*.fna) and gene co-ordinate files (*.ptt) for target and reference genomes. The clustered-upstream DNA sequences can be used by motif prediction tool, such as MEME, Bio-prospector, Gibbs motif sampler, MDscan for prediction of conserved DNA elements. We tested the performance of UpCoT by selecting the genome of Synechocystis sp PCC 6803 as the target and 13 different cyanobacterial genomes as reference. The clustered upstream sequences generated by UpCoT of groES, ycf24 and nirA were used for cis-regulatory element prediction. The results were consistent with the experimentally identified cis-regulatory elements. Therefore, UpCoT is a reliable and automated pipeline package for prediction of orthologs, orthologous transcriptional units, and orthologous upstream sequences of a selected prokaryotic genome. UpCoT can be downloaded from http://jssplab.uohyd.ac.in/upcot/.
Highlights
IntroductionDNA sequencing technologies, a number of microbial genomes have been sequenced during the past decade and the sequence information is available in various genome databases
With the advent of fast and generation automatedDNA sequencing technologies, a number of microbial genomes have been sequenced during the past decade and the sequence information is available in various genome databases
The clustered-upstream DNA sequences can be used by motif prediction tool, such as MEME, Bio-prospector, Gibbs motif sampler, MDscan for prediction of conserved
Summary
DNA sequencing technologies, a number of microbial genomes have been sequenced during the past decade and the sequence information is available in various genome databases. Phylogenetic footprinting is one of the widely accepted computational method for predicting cis-regulatory elements for a given genome in question (Hardison 2000). This method can be considered as a two step process. Various computational tools, such as MEME, Bioprospector, Gibbs sampler, MDScan are used for predicting conserved. The number of microbial genomes being sequenced is constantly increasing and demands for the development of an automated tool Developing such a tool would facilitate the biologists to work on any microbial genome for quick generation of clustered-upstream DNA sequences for the target genome in question. The output of the UpCoT can be directly used for prediction of cis-regulatory elements using any computational tool of user’s choice
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