GeSeq - Release Notes

Version

Online

Release Notes

1.00

09 May 2017

• Version published in Nucleic Acids Res (2017) 45: W6-W11

1.20

15 May 2017

• NCBI RefSeq

  • improved search

    • faster

    • free text search

      • more than one expression can be searched

      • accepts common species names

• Output

  • ​empty annotation output was removed

    • if GeSeq cannot identify genes or features in a sequence "no annotation" is displayed

13 Jun 2017

• ARWEN

  • basic implementation, runs with default parameters only

  • table and graphical output

• ARWEN
  • graphical output removed
• GenBank file
  • FEATURE section
    • ARWEN output (default parameters) is written in GenBank file
  • COMMENT section
    • GeSeq version is logged
    • harmonization of spellings
• OGDRAW
  • jpg instead of png output​

• GUI revision 

• OGRAW
  • ​bug fix: download button for jpg is now working in Edge

• tRNA predictors
  • update of ARAGORN to v1.2.38
  • ARWEN and ARAGORN use now internal parameter "-c" (for circular sequences) instead of processing a simulated circular input sequence
  • bug fix: GeSeq was made more robust against "unusual" tRNAs identifed by the predictors 
  • bug fix: tRNAs that span the ends of the submitted linear sequence identifed by tRNAscan-SE are now correctly written in the GenBank output

• ARWEN
  • search parameters are now enabled

• ARAGORN
  • uses for intron search now the internal parameter "-i" instead of "-ifo" as default setting 
  • more intron search parameters are now enabled
  • reports now low scoring tRNAs as optional feature

• tRNAscan-SE
  • Echinoderm Mitochondria genetic code enabled

• tRNAscan-SE
  • a ​warning against very long runtimes is now displayed, if tRNAscan-SE v1.3.1 is activated in its Mitochondrial/Chloroplast tRNA search mode​
• OGDRAW
  • bug fix: passing of output file to the front-end was made more robust
• GenBank file
  • ​bug fix: empty line​s after translation are no longer possible
• ​Upload
  • ​GeSeq is now more robust against files in unusual FASTA formats
  • CDS in custom Genbank files without a single translation entry are now used for the local BLAT database

• Upload​
  • GeSeq parses now NCBI FASTA Nucleotide headers of CDS sequences and automatically converts them into the GeSeq synthax
  • GeSeq is now more robust against the upload of GenBank files in an unusual format or the upload of protein sequences

• tRNA predictors
  • up​date of tRNAscan-SE to v2.0
  • update of ARWEN to v1.2.3
  • selection of genetic codes for ARWEN and ARAGORN is now limited to the organelles/organisms for which tRNA prediction of these programs is optimized

• GenBank file
  • ​​selection of seach parameters is now logged in a machine-readable format in the GenBank header

• OGDRAW
  • ​update to v1.2.1 which fixes several bugs conneted with the communicaion of GeSeq und OGDRAW
• Upload
  • ​implementation of a chloroplast and mitochondrial genome annotation mode

• HMMER
  • if HMMER search runs alone (without selection of BLAT references), hits are now annotated as genes (CDS and rRNA) and no longer as misc_features

• OGDRAW
  • ​bug fix: the plastid inverted repeat is now only drawn for chloroplast genomes and only if its identification was selected by the user

• Output
  • emtpy multi-FASTA output was removed

• NCBI RefSeq
  • improved search functions

30 Jul 2018

• Output
  • GeSeq can now create multi-GenBank files as optional feature
• GenBank file
  • GeSeq logs now the date in the first line of the GenBank file​

• OGDRAW
  • ​update to v1.3 which fixes several bugs:
    • IR_A and IR_B are now displayed in the correct order on the map
    • genes with introns are now labeled with *
    • OGDRAW can now deal with a degenerated nucleic acid code, such as Ns

• ARAGORN
  • ​bug fix: exon/intron boarders are now written correctly

• Upload
  • OGDRAW is now more robust against unusual characters in the FASTA header
• Erorr log
  • implementation of an error log file
  • missing ODGRAW output is logged
  • the user is notified, if FASTA files with identical headers are uploaded; this leads to overwriting of output files by GeSeq

• GenBank output
  • pseudo-GenBank files produced by GeSeq now better reassemble NCBI GenBank flatfiles​

• OGDRAW
  • draws now the plastid inverted repeat as identifed by GeSeq and no longer as identifed by its internal algorithm

• OGDRAW
  • bug fix: OGDRAW was made more against multiple parallel jobs run on the GeSeq Server

• OGDRAW
  • update to v1.4
  • OGDRAW can now draw features that span the ends of the submitted linear sequence - an exception is still the IR

• OGDRAW
  • OGDRAW can now draw an IR that spans the ends of the submitted linear sequence correctly

• tRNA predictors
  • GeSeq reports now a scores for all tRNAs identifed de novo, including those found by ARAGORN and ARWEN

• Output
  • GFF3 output for GeSeq was implemented
• BLAT
  • GeSeq reports now the BLAT pls score

• GenBank file
  • GeSeq collapses now identical annoations of the same feature into one GenBank entry

• Annotation
  • if possible, GeSeq applies now the naming convention trnAMINO ACID ONE LETTER CODE-ANTICODON, e.g. trnA-GCC, to all annotated tRNAs

• Ouput
  • raw BLAT results can now provided as optional feature
  • GeSeq can now create multi-GFF3 files as optional feature

• BLAT
  • the "find short matches" option was disabled

• tRNA predictors
  • up​date of tRNAscan-SE to v2.0.3
• Chloroplast mode
  • annoation of the psaA gene duplication in psaB and vice versa is now obmitted
  • the transpliced gene rps12 in chloroplast genomes is now annoated as such

• Upload
  • GeSeq was made more robust for filtering (organelle genome) contigs from raw assemblies
    • ​huge assembiles can now be proccessed, however
      • file upload is limited to 250 MB
      • GeSeq automatically stops jobs when occupying to much server capacity​

• Annotation
  • if possible, GeSeq applies now the naming convention rrnSIZE IN SVEDBERG UNITS without the "S", e.g. rrn16, to all annotated rRNAs

• Annotation
  • genes annoated in a reference only as "locus_tag" or "orf" can now be ignored by GeSeq as optional feature

• Output
  • GeSeq provides now its annotation output also in the GBSON format, a new annotation file format based on JSON, containing all information stored in a GenBank Flat File but with advantageoius parsing and information structure properties

• Output
  • the GeSeq output is now stuctured according to file type and function

• tRNA predictors
  • up​date of tRNAscan-SE to v2.0.5

• Upload
  • GeSeq can now read ENA files (*.embl or *.ena)

•  Annotation
  • GeSeq now writes LSC, SSC, IRA and IRB

• tRNA predictors
  • GeSeq now correctrly recognizes trnO, trnU and trnTERM

• Output
  • GeSeq now clearly labels the origin of every annotation in the GenBank and GBSON format using the custom qualifier "annotator"
  • in the GenBank and GBSON output the quality of an annotation is now described by the custom qualifier "info"

• HMMER
  • update to v3.3.1
• tRNA predictors
  • update of tRNAscan-SE to v2.0.6
• BLAT
  • update to v36x2

• Stand-alone annotators
  • GeSeq has now implemented the stand-alone annotators Chloë and MFannot to support (and correct) de novo annotations derived from BLAT or HMMER and/or the tRNA predictors tRNAscan-SE, ARAGORN or ARWEN
  • MFannot running under the umbrella of GeSeq is not yet open to the public

• tRNA predictors
  • update of tRNAscan-SE to v2.0.7

• GenBank file
  • ​for land plant chloroplasts GeSeq now writes gene product names

• Annotation
  • GeSeq now evaluates CDS annotations of Chloë, BLAT, or HMMER and picks the best one as a default feature