This page contains supplementary information to the following paper:

Zasha Weinberg and Walter L. Ruzzo, "Sequence-based heuristics for faster annotation of non-coding RNA families", Bioinformatics, to appear.

Software

The software is here

Supplementary paper

Raw ROC-like Curves

The raw points for the ROC-like curves are supplied as comma-separated files.  The first column is the sensitivity, the second is the filtering fraction and the third is the heuristic threshold score (in log_2 units) to obtain this sensitivity & filtering fraction.

The complete set is available tar'd and gzip'd: here (3 MB).  The file names are described below.

Rfam families ROC-like curves

All files end in ".posvsfrac.csv".

The first part of the file name is the Rfam ID: RF00001, RF00005, RF00010, RF00029, RF00031, RF00059, RF00168 or RF00174.

The next part of the file name describes what filter was tested:

• "" (nothing) : ML-heuristic
• "_expandedMlPath" : ML-heuristic with expanded-type HMM (only for RF00005)
• "_expandedRigor" : expanded-type rigorous profile HMM
• "_fakeCmbuild" : ignore-SS
• "_full90id_mlPath" : ML-heuristic trained on the full Rfam members, filtered to <90% identity between pairs of sequences.
• "_rfamseed-5.0-BLAST-1sided": 1-sided BLAST on seed members of Rfam
• "_rfamseed-5.0-BLAST-2sided": 2-sided BLAST on seed members of Rfam
• "_rfamseed-5.0_evalue1-BLAST-1sided": 1-sided BLAST on seed members of Rfam, run with lower E-value of 1, to assess how accurate ROC-like curves are for BLAST.  (Only for RF00005.)
• "-BLAST-1sided": 1-sided BLAST on full Rfam members, filtered to <90% identity between pairs of sequences.
• "-BLAST-2sided": 2-sided BLAST on full Rfam members, filtered to <90% identity between pairs of sequences.

tRNAscan-SE scans

All files end in ".posvsfrac.csv".  All files use compact-type ML-heuristic.

For historical reasons, the prokaryote files begin with "TRNA2" while the eukaryote files begin with "tRNAscan-TRNA2".  Next the organism(s) is specified:

• "arch" : archaeal
• "bact" : eubacterial
• "euk_Celegans": C. elegans (nuclear genome only)
• "euk_Drosophila": Drosophila (nuclear genome only)
• "euk_human": human (nuclear genome only)

Next, the window length for the ML-heuristic is given:

• win100: window length W=100
• win500: window length W=500

Other data on tRNAscan-SE scans of these same databases are available from our previous paper; see this Web supplement.