NCBI IgBLAST : Release notes

Oct 18, 2023

Release 1.22.0

*Improved CDR3/FR4 boundary detection by allowing non-exact match to the first 3 nucleotides of the FR4 region in J genes. The purpose of this is to accommodate possible nucleotide variation/deletion introduced by D-J and V-J rearrangement as well as mutation events.

*Improved V gene amino acid sequence translation of individual FR/CDR regions for AIRR rearrangement format when there is internal frame shift in V gene. Previously the amino acid sequence was translated from the corresponding individual FR/CDR region without considering frame shift that possibly exists at some FR/CDR boundary.

Mar 7, 2023

Release 1.21.0

*Added gaps to *_alignment_aa fields (such as sequence_alignment_aa) to reflect gaps in nucleotide sequence alignment.

*Added the new AIRR format field: sequence_aa. This is direct translation (no gaps) of nucleotide sequence using the reading frame determined by nucleotide sequence alignment to its closet germline V gene.

*Added the new AIRR format field: d_frame. This is the D gene frame that is in-frame with the J gene coding frame. IgBLAST offers built-in IGHD gene frame support for mouse as defined by Ichihara Y et al (European Journal of Immunology Volume 19, Issue 10 p. 1849-1854). Users can use their own custom D gene definition with IgBLAST according to their needs.

Oct 18, 2022

Release 1.20.0

*Added capability to use custom V gene FWR/CDR annotation

Jun 02, 2022

Release 1.19.0

*Added logic to handle the case where there is an unrearranged J gene downstream of the VDJ rearrangement.

Dec 13, 2021

Release 1.18.0

*Added capability to report C genes for Ig sequences.

Feb 26, 2021

Release 1.17.1

*Fixed annotation errors for TCR J genes.

Oct 16, 2020

Release 1.17.0

*Added the V frame shift field to indicate if there is an internal frame shift in V gene translation frame (for example, nucleotide deletions/insertions found in pseudogenes or caused by somatic mutations).

*The definition for whether a sequence is productive or not has now been updated. Previously, a sequence is considered to be productive if the V(D)J rearrangement frame is in-frame and no stop codon is found. Now the definition for a productive sequence includes no internal frame shift in V gene, in addition to previous requirement of V(D)J rearrangement frame being in-frame and no stop codon.

Apr 17, 2020

Release 1.16.0

*Added ability to use custom organism.

*Added ability to extend J gene alignment at 3’ end.

*Added the AIRR complete_vdj field.

*Deleted parameters that are used for standard BLAST but not for IgBLAST.

Jan 21, 2020

Release 1.15.0

*Added support for the FWR4 annotation.

*The previous “-penalty” parameter was renamed as V_penalty to be consistent with other IgBLAST penalty options

*Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) such that this process is not influenced by user parameters

*Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.

Apr 29, 2019

Release 1.14.0
Making AIRR format more consistent with AIRR specs including changing undefined type (NON, N/A) to empty string, not appending “reversed” to seqid when query is in reversed orientation, using standard locus names such as IGH, TRB instead of traditional VH, VB etc.
Loosening criteria to show CDR3 end by allowing the first FWR4 base to be missing.
Bug fix: Restoring seqid for no result case in AIRR rearrangement format. Printing IgBlast version number instead of Blast version number with -version option.

Mar 7, 2019

Release 1.13.0
Determine the V gene reading frame from the end of FWR3 region instead of end of V gene. This is to allow proper determination of the frames for rearrangements that have insertions or deletions near the V gene end.
Increase allowed distance between V gene end and J gene start to 225 bp to allow detection of ultra long D/N region.
Package the edit_imgt_file.pl script, the internal_data and optional_files folders into the IgBlast release such that it is easy for u ser to install.

Nov 26, 2018

Release 1.12.0
Increase allowed distance between V gene end and J gene start positions (from 90 bp to 150 bp) as well as between V gene end and D gene start positions (from 55 to 120 bp) to accommodate extremely long VDJ junctions found in some antibodies.

Oct 25, 2018

Release 1.11.0
Change the 0-based coordinate system to 1-based coordinate system in AIRR format (with -outfmt 19 parameter) for sequence start positions per the new AIRR Rearrangement Schema ( http://docs.airr-community.org/en/latest/datarep/rearrangements.html ).

Aug 24, 2018

Release 1.10.0
Fix some processes not exiting under cpu full load condition

April 30, 2018

Release 1.9.0
Adding the AIRR rearrangement tabular format

Sept 22, 2017

Release 1.8.0.
Re-engineered multi-threading mechanism which significantly shortens the processing time. Default t o use 4 threads.
Added ability to accept the SRA accession directly as query input.
Lower the default nucleotide mismatch penalty values for finding D and J genes (from -4 to -2 and f rom -3 to -2, respectively). This is to better accommodate moderately mutated sequences.

April 19, 2017

Release 1.7.0.
Make nucleotide overlaps at VDJ junctions an option (-allow_vdj_overlap) and default is set to no o verlap allowed. Previous versions were hard-coded to allow nucleotide overlaps at VDJ junctions. *Use alignment length instead of percent identity as tiebreaker for hits with identical blast scores .
Allow custom J gene mismatch penalty.
Add CDR3 start and stop to sub-region table

Oct 26, 2016

Release 1.6.1
Added clonotype report
Enabled multi-threading option -num_threads

April 25, 2016

Release 1.5.0
Added CDR3 annotation
Added option for extending at 5’ side
Default to IMGT region (was Kabat previously)

July 17, 2014

Release 1.4.0
Added capability to analyze monkey sequences.

February 19, 2014

Release 1.3.0
Better handling of non-Ig sequences
Include makeblastdb binary with pre-compiled releases

NCBI IgBLAST B and T cell domains

Release notes