miRNAture/Changes at main · Bierinformatik/miRNAture · GitHub

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Revision history for Bio-miRNAture

1.1    Sept 21 2022.
        # Updates
        - Using blast+ for all pairwise comparisons. Reeplaced blast legacy.
        - Implemented subseting HMMs and CMs as symlinks to be run in parallel.
        - Correction warning messages when miRNAture did not found candidates.
        - All modes run in parallel using:
          O. Tange (2018): GNU Parallel 2018, Mar 2018, ISBN 9781387509881, DOI https://doi.org/10.5281/zenodo.1146014
        - hmm searches now running by default rfam, mirbase (and user) models.
        - Re-organized homology running modes from:
            Blast,HMM,Infernal,OTHER_CM,Final
          to
            blast,hmm,rfam,mirbase,user,final
        - Transverse search added to find specific files over folders.
        - Included flag '-nbitscore_cutoff' which control the normalized bitscore threshold (nBit).
          nBit = Bitscore / Defined-gathering-score.
        - Included 'no_homology' search mode to perform validations and subsequent analysis.
        - Support of multiple runs at the same time without I/O temporal files collision.
        - Automatic creation of output folder declared on the -w flag.
        - Inclusion of a global alignment (cmsearch -g) to validate structural curated sequences in
          comparison to reference covariance model (from structural evaluation if available or
          used on the homology stage).
        - Extension of homology fasta sequences before structural validation with MIRfix.
        - Search on genome intervals and not in the complete genome. MIRfix is faster looking for candidates and
          re-mapping correct candidates is done on previous calculated genome regions.
        - Added -E 0.015 to get valid candidates. Since the pipeline is not dealing with candidates that reported
          greater E-values.
        - Broken evaluation could be restarted, miRNAture evaluates folder structure and structurally evaluate
          candidates.
        ### Corrected bugs
        - Temporal file folders moved to TemporalFiles/ folder.
        - Corrected cleaning of temporal files.
        - Remove of genome.txt file and related functions.

1.00    Feb 1 2021.
        First version, released on an unsuspecting world.