v1.0.0

v1.0.0 introduces the following major upgrades:

• Receptor detection:

  • The library of HMMs for TPRs has been updated using the HMMs present in interproscan-5.56-89.0
  • 20 additional HMMs of TPRs from Pfam have been included: TPR_1 (PF00515.30), TPR_2 (PF07719.19), TPR_3 (PF07720.14), TPR_4 (PF07721.16), TPR_5 (PF12688.9), TPR_6 (PF13174.8), TPR_7 (PF13176.8), TPR_9 (PF13371.8), TPR_10 (PF13374.8), TPR_11 (PF13414.8), TPR_14 (PF13428.8), TPR_15 (PF13429.8), TPR_16 (PF13432.8), TPR_17 (PF13431.8), TPR_18 (PF13512.8), TPR_19 (PF14559.8), TPR_20 (PF14561.8), TPR_21 (PF09976.11), TPR_22 (PF18833.3) and TPR_MalT (PF17874.3)
  • The tprpred software has been integrated and can be called in complement of hmmsearch to increase the sensitivity of the tool
  • An HMM of the AimR family has been built and is now used to identify these receptors with more sensitivity

• Propeptide detection:

  • The main improvement of v1.0.0 lies in a new algorithm to detect small peptides encoded in the vicinity of receptors, as such small peptides are typically absent from annotation files. We called this method SPRAT for Small Peptides with RBS Annotation Tool. This method identifies peptides preceded by a Shine-Dalgarno RBS in the flanking regions of each receptor, using the 27 hierarchical regular expressions introduced by Prodigal to detect SD-RBS motifs. This is justified by the fact that 90% of the canonical genes encoded by Firmicutes have an SD-RBS upstream. Optionally, the user can submit a list of possible start codons to consider for the detection of putative small pepite-coding ORFs (by default, only ATG is considered).
  • The PrediSi software has been integrated an can be called in complement of SignalP to increase the sensitivity of the tool
  • An HMM of SHP propeptides has been built and is now used to identify SHP propeptides since SHPs are not exported via the SEC-translocon and are therefore not returned by SignalP or PrediSi

• Iterative Search:

  • When the target database is large, it may be relevant to use the detected systems as baits to fish homologous systems that did not pass the conservative thresholds of RRNPP_detector. If this option increases the sensitivity of the tool, it also increases the risk of false positives

v0.0.1

This is the initial release of RRNPP_detector.