Open Access Highly Accessed Research article

Analysis of the unexplored features of rrs (16S rDNA) of the Genus Clostridium

Vipin Chandra Kalia*, Tanmoy Mukherjee, Ashish Bhushan, Jayadev Joshi, Pratap Shankar and Nusrat Huma

Author Affiliations

Microbial Biotechnology and Genomics, Institute of Genomics and Integrative Biology (IGIB), CSIR, Delhi University Campus, Mall Road, Delhi-110007, India

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BMC Genomics 2011, 12:18  doi:10.1186/1471-2164-12-18

Published: 11 January 2011

Additional files

Additional file 1:

Table S1 Clostridium species. File contains rrs sequences of Clostridium species which occurred with low frequency and the number of sequences used in this study http://rdp.cme.msu.edu/ webcite.

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Additional file 2:

Figures S1-S15 'Guide trees' for phylogenetic famework. File contains 'Guide trees' for all the 15 Clostridium spp. used to develop phylogenetic framework sequences for this study.

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Additional file 3:

Figure S16 Phylogenetic tree of 16S rDNA of Clostridium spp. and Framework sequences. File contains a neighbor - joining analysis of rrs sequences of Swine fecal bacterium, Clostridiaceae bacterium and unidentified eubacterium - 31 along with 56 of phylogenetic framework.

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Additional file 4:

Tables S2-S3 'Novel' and low frequency Clostridium spp. File contains representative rrs sequences of unsegregated Clostridium sp. (novel) and Clostridium spp. with small population sizes.

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Additional file 5:

Figure S17 Phylogenetic tree of 84 16S rDNA sequences of 'novel' Clostridium species. File contains a neighbor - joining analysis of 56 representative novel Clostridium sequences.

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Additional file 6:

Figures S18-S19 Phylogenetic tree of 16S rDNA of novel Clostridium spp. and low frequency Clostridium spp. File contains a neighbor - joining analysis performed on the rrs sequences of novel Clostridium sp. (Additional file 4: Table S2) 56 along with 83 representatives of Clostridium sp. known to occur at low frequency (Additional file 4: Table S3).

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Additional file 7:

Table S4 RE sites with low frequency. File contains low frequency in silico Restriction Enzymes cut sites in rrs sequences of different Clostridium spp.

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Additional file 8:

Figures S20-S36 Regular expression diagram. File contains regular expression diagram of signatures (nucleotides) of rrs sequences of 15 Clostridium spp. obtained through MEME suite.

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Additional file 9:

Table S5-S21 Motifs for 15 Clostridium spp. File represents motifs obtained for Clostridium botulinum (128 rrs sequences) through MEME suite and the frequency of their occurrence across other Clostridium spp. using BioEdit.

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Additional file 10:

Table S22 Nucleotide signatures. File contains nucleotide signatures of rrs sequences common to Clostridium sp. used for developing framework sequences.

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Additional file 11:

Tables S23-S26 Representative motifs for Clostridium botulinum and C. perfringens. File contains details of rrs sequences of Clostridium botulinum and C. perfringens used for drawing Regular Expression Diagram of signatures presented in Additional file 8: Figures S20-S23.

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