The biggest change since the last release is the renaming of SLiMSearch to SLiMProb. This is to avoid confusion between the old SLiMSearch 1.x (now SLiMProb) and the newer SLiMSearch 2.x webserver, which has a different range of functions.
Updates since last release:
• cpppred: Created.
• gopher: Updated from Version 3.1.
→ Version 3.2: Minor tweak to prevent unwanted directory generation for programs using existing GOPHER alignments.
→ Version 3.3: Added rje_blast_V2 to use BLAST+. Run with legacy=T to stick with old NCBI BLAST. Started utilising rje_seqlist.
• pepbindpred: Created.
• slimprob: Created.
→ Version 1.0: SLiMProb 1.0 based on SLiMSearch 1.7. Altered output files to be *.csv and *.occ.csv.
• file_monster: Updated from Version 2.0.
→ Version 2.1: Added dirsum function.
• rje: Updated from Version 4.5.
→ Version 4.6: Added dev and warn options.
• rje_blast_V2: Created.
→ Version 2.0: Initial Compilation from rje_blast_V1 V1.14.
→ Version 2.1: Tweaking code to work with GOPHER 3.x - removing self.info etc. Added blastObj() method.
• rje_db: Updated from Version 0.4.
→ Version 0.5: Initial coding of index mode. (Not yet fully functional.)
→ Version 1.0: Working, so upgraded to version 1.0!
• rje_obj: Updated from Version 0.0.
→ Version 1.0: Fully working version, so upgraded to 1.0. Added dev and warn options.
• rje_seq: Updated from Version 3.15.
→ Version 3.16: Added BLAST+ path and seqFromBlastDBCmd()
• rje_slimcalc: Updated from Version 0.5.
→ Version 0.6: Minor tweak to avoid unwanted GOPHER directory generation.
→ Version 0.7: Added RLC to "All" conscore running.
• rje_slimcore: Updated from Version 1.9.
→ Version 1.10: Bypass UPC generation for single sequences.
Documentation is still in the process of development. BLAST+ implementation is ongoing - please get in touch if this is something you need.