Systematic identification of stem-loop containing sequence families in bacterial genomes.

BMC Genomics
Luca CozzutoGiovanni Paolella

Abstract

Analysis of non-coding sequences in several bacterial genomes brought to the identification of families of repeated sequences, able to fold as secondary structures. These sequences have often been claimed to be transcribed and fulfill a functional role. A previous systematic analysis of a representative set of 40 bacterial genomes produced a large collection of sequences, potentially able to fold as stem-loop structures (SLS). Computational analysis of these sequences was carried out by searching for families of repetitive nucleic acid elements sharing a common secondary structure. The initial clustering procedure identified clusters of similar sequences in 29 genomes, corresponding to about 1% of the whole population. Sequences selected in this way have a substantially higher aptitude to fold into a stable secondary structure than the initial set. Removal of redundancies and regrouping of the selected sequences resulted in a final set of 92 families, defined by HMM analysis. 25 of them include all well-known SLS containing repeats and others reported in literature, but not analyzed in detail. The remaining 67 families have not been previously described. Two thirds of the families share a common predicted secondary structure an...Continue Reading

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Citations

Dec 25, 2009·Bioinformatics·Shang-Hong Zhang, Ya-Zhi Huang
Aug 2, 2013·BMC Genomics·Pier Paolo Di NoceraFrancesco Rocco
Apr 28, 2009·FEMS Microbiology Reviews·Todd J TreangenEduardo P C Rocha
Feb 19, 2009·FEMS Microbiology Letters·Eliana De GregorioPier Paolo Di Nocera

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Software Mentioned

RANDFOLD
RNAz
MCL
REP
HMMBUILD
ALISTAT
HMMER
HMMALIGN
HMMCALIBRATE
PCMA

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