Similar protocols

Pipeline publication

[…] ble of gene neighbors centered on a query gene. Then the BLASTCLUST program is used to cluster products in the neighborhood and establish conserved co-occurring genes. These conserved gene neighborhoods are then sorted as per a ranking scheme based on occurrence in at least one other phylogenetically distinct lineage ("phylum" in NCBI Taxonomy database), complete conservation in a particular lineage ("phylum") and physical closeness on the chromosome indicating sharing of regulatory -10 and -35 elements. Profile searches were conducted using the PSI-BLAST program [] with a default profile inclusion expectation (E) value threshold of 0.01. Profile-profile comparisons were performed using the HHpred program []. HMM searches were conducted using the newly released HMMER3 program []. Multiple alignments were constructed using Kalign [] followed by manual adjustments based on PSI-BLAST results. Protein secondary structure was predicted using a multiple alignment as the input for the JPRED program []., The authors declare that they have no competing interests., LMI and LA were involved in the discovery process. RdeS and LA performed the analysis. RdeS and LA wrote the paper. The figures were prepared by RdeS and LMI. All authors have read and approved the final manuscript., M. Madan Babu, MRC Laboratory of Molecular Biology, University of Cambridge, UK., In this manuscript, De Souza, Iyer and Aravind report the characterization of a family of proteins which are related to the Anabena sensory rhodopsin transducer. T […]

Pipeline specifications

Software tools HHPred, HMMER, Kalign
Databases NCBI Taxonomy Database