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GeSeq - Release Notes


Since its publication GeSeq has received the following updates:

 

Version

Online

Release Notes

1.00

09 May 2017

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

1.30

13 Jun 2017

  • ARWEN

    • basic implementation, runs with default parameters only

    • table and graphical output

1.35 21 Jun 2017
  • 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​
1.36 04 Jul 2017
  • GUI revision 
1.37 08 Aug 2017
  • OGRAW
    • ​bug fix: download button for jpg is now working in Edge
1.38 18 Aug 2017
  • 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
1.39 06 Sep 2017
  • ARWEN
    • search parameters are now enabled
1.40 15 Sep 2017
  • 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
1.41 19 Sep 2017
  • tRNAscan-SE
    • Echinoderm Mitochondria genetic code enabled
1.42 10 Nov 2017
  • 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
1.43 04 Dez 2017
  • 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
1.50 28 Feb 2018
  • 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
1.51 04 Apr 2018
  • GenBank file
    • ​​selection of seach parameters is now logged in a machine-readable format in the GenBank header
1.52 10 Apr 2018
  • 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
1.53 18 Apr 2018
  • 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
1.54 30 May 2018
  • OGDRAW
    • ​bug fix: the plastid inverted repeat is now only drawn for chloroplast genomes and only if its identification was selected by the user
1.55 12 Jun 2018
  • Output
    • emtpy multi-FASTA output was removed
1.56 24 Jul 2018
  • NCBI RefSeq
    • improved search functions
1.57

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​
1.58 01 Aug 2018
  • OGDRAW
    • ​update to v1.3 which fixes several bugs:
      • IRA and IRB 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
1.59 02 Aug 2018
  • ARAGORN
    • ​bug fix: exon/intron boarders are now written correctly
1.60 07 Aug 2018
  • 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
1.61 09 Aug 2018
  • GenBank output
    • pseudo-GenBank files produced by GeSeq now better reassemble NCBI GenBank flatfiles​
1.62 10 Aug 2018
  • OGDRAW
    • draws now the plastid inverted repeat as identifed by GeSeq and no longer as identifed by its internal algorithm
1.63 14 Aug 2018
  • OGDRAW
    • bug fix: OGDRAW was made more against multiple parallel jobs run on the GeSeq Server
1.64 20 Sep 2018
  • 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
1.65 10 Oct 2018
  • OGDRAW
    • OGDRAW can now draw an IR that spans the ends of the submitted linear sequence correctly
1.67 5 Feb 2019
  • tRNA predictors
    • GeSeq reports now a scores for all tRNAs identifed de novo, including those found by ARAGORN and ARWEN
1.68 05 Apr 2019
  • Output
    • GFF3 output for GeSeq was implemented
  • BLAT
    • GeSeq reports now the BLAT pls score
1.69 11 Apr 2019
  • GenBank file
    • GeSeq collapses now identical annoations of the same feature into one GenBank entry
1.70 23 Apr 2019
  • Annotation
    • if possible, GeSeq applies now the naming convention trnAMINO ACID ONE LETTER CODE-ANTICODON, e.g. trnA-GCC, to all annotated tRNAs
1.71 30 Apr 2019
  • Ouput
    • raw BLAT results can now provided as optional feature
    • GeSeq can now create multi-GFF3 files as optional feature
1.72 09 May 2019
  • BLAT
    • the "find short matches" option was disabled
1.73 22 May 2019
  • 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
1.74 26 Jun 2019
  • 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​
1.75 01 Aug 2019
  • Annotation
    • if possible, GeSeq applies now the naming convention rrnSIZE IN SVEDBERG UNITS without the "S", e.g. rrn16, to all annotated rRNAs
1.76 13 Aug 2019
  • Annotation
    • genes annoated in a reference only as "locus_tag" or "orf" can now be ignored by GeSeq as optional feature
1.77 10 Oct 2019
  • 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
1.78 02 Dec 2019
  • Output
    • the GeSeq output is now stuctured according to file type and function
1.79 29 Jan 2020
  • tRNA predictors
    • up​date of tRNAscan-SE to v2.0.5
1.80 12 Mar 2020
  • Upload
    • GeSeq can now read ENA files (*.embl or *.ena)
1.81 22 Apr 2020
  •  Annotation
    • GeSeq now writes LSC, SSC, IRA and IRB
1.82 11 May 2020
  • tRNA predictors
    • GeSeq now correctrly recognizes trnO, trnU and trnTERM
1.83 27 Aug 2020
  • 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"
1.84 31 Aug 2020
  • HMMER
    • update to v3.3.1
  • tRNA predictors
    • update of tRNAscan-SE to v2.0.6
  • BLAT
    • update to v36x2
2.00 10 Oct 2020
  • 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