User:Patingan/sandbox

[rfam name] is a non-coding small RNA that was initially discovered in the pathogenic bacteria Staphylococcus aureus subsp. aureus N315 by RNA-seq coverage. The seed sequence, called Sau-5995, has been reported with an RNA-seq coverage equal to 414.

The [rfam name] gene is conserved in the genome of many Staphylococcaceae familly species, such that Staphylococcus aureus, warneri, epidermidis, saprophyticus, haemolyticus, pseudintermedius, pasteuri or lugdunensis (homologues found with the NCBI Blastn tool against the non-redondant database).

We can also remarkes that a paralogue sequence is always detected in the aureus species genomes, but not for the other species.

Alignment protocol
The overall protocol is based on the document "Screening Genome Sequences for known RNA Genes or Motifs" from D.Gautheret, Orsay 2011.

Initial sequence Sau-5995 (93bp sized) was BLASTed against non-redondant database (NCBI blastn). 122 hits were found with significant e-value (<0.01), including a set of 18 sequences which are all different from each other. From the multiple alignment of the previous 18 sequences (computed with Locarna) a nucleotide HMMER (with default parameters, 0.01 e-value threshold) research was performed against all the currently available bacterial genomes (which database version ??), but no new hit was found. Then, the INFERNAL tool (with default parameters, 0.01 e-value threshold) found one more sequence. Finally, a HMMER and INFERNAL cycle was performed on the newly 19 sequences multiple alignment, however no new significant hit was found.

Structure
A run with the Locarna online tool (with default parameters and the previous multiple alignment as input) show a well defined secondary structure. The 22 predicted pair-base matching includes 4 match with 3 co-mutations and 7 match with 2 co-mutations.

Flanking genes
Among the 122 hits discovered by Blastn, 59 are extracted from already annotated genomes. For 41 of these hits, a "cold shock protein" is found between 20 and 30 pair-base at 3' side, which could be in favor with an interaction between this two genes.