iHMMune-align web-based access

Help, FAQs and Further Information

iHMMune-align Change Log

10th, January, 2008

  • Added fix for use of custom scoring matrices

7th, Sepember, 2007

  • Added the dprob column to the CSV output header as it was missing
  • Fixed display of hotspots whose nucleotides span across the gaps introduced to allow for IMGT numbering of the IGHV region
  • Updated the output options and the output documentation pages

6th, September, 2007

  • Added description of Combined Repertoire Option
  • Fixed 'fatal error' that was resulting when attempting to display mutation information for sequences with stop codons present
  • Edited gapping template and combined repertoire files to ensure consistient nomenclature with the IGHV-R1, as inconsistiencies were causing some sequences not to be gapped
  • Added contact emails to the navigation menu

2nd, September, 2007

  • Altered iHMMune-align to correctly output multiple IGHV (if requested) for sequences where the first IGHV found has gaps present
  • Added option to use choose between the IGHV Expressed Repertoire and a combined repertoire based on merging of the iHMMune-align, IMGT and VBASE2 repertoires
  • Added IMGT numbering of mutation output for the IGHV of input sequences
  • Added CDR/FR delimiters to the IGHV for mutation display
  • Edited general site layout, simplified iHMMune-align submission form and added download section

23rd, July, 2007

  • Fixed an error that was preventing the return of alignments where the input sequences was lacking either the N1 or N2 region

11th, July, 2007

  • Altered iHMMune-align to identify gaps in the input sequence, HMM not yet able to deal with gaps but prints message to indicate their presence
  • Fixed rounding of IGHD misidentification probabilities to improve display
  • Fixed problems with display of mutation alignment when multiple IGHV are being displayed for a single sequence

9th, July, 2007

  • Added 'Dynamic' option for determination of IGHD gene identification criteria
  • Added IGHD misidentification probabilities (as described in Jackson, 2007) to the iHMMune-align algorithm
  • Fixed in-line table errors that were causing display problems in Microsoft Internet Explorer

6th, July, 2007

  • Added mutation display and summary of mutation paths as an output option
  • Updated iHMMune-align algorithm to allow return of multiple IGHV alternatives for a sinlge input sequence

7th, June, 2007

  • Added save button to results page to download CSV results as a text file to local computer
  • Fixed 'Summary of Results' display for sequences that lack an indentifiable IGHD
  • Added documentation pages: minJ, range, seqs per run, IGHD identification
  • Added 'HTML' as an output format option
  • Added 'header' to CSV output to describe column contents

31st, May, 2007

  • Changed Scoring Matrix options to a drop down box
  • Added output of iHMMune-align execution details to a text area when an error occurs to make trouble shooting easier
  • Changed 'Output Summary' to side-by-side box design

30th, May, 2007

  • First version of iHMMune-align Web-based access
Contact

For queries about iHMMune-align:
Andrew Collins
Katherine Jackson