Tag: Immunoglobin

Web IgBLAST can now determine immunoglobulin isotypes

We have added a new function to IgBLAST on the Web. You can now search immunoglobulin (Ig) nucleotide sequences against the Constant region (C) gene database (Figure 1) to determine the Ig isotypes including subtypes (IgM, IgG, IgA1, etc.). The isotype information is reported in the rearrangement summary table, and the C gene region is displayed in the alignment section. This feature is now available on the IgBLAST web service for human and mouse sequences with possible expansion to other organisms in the future.  The feature is not yet implemented for the standalone IgBLAST package.

Figure 1.  IgBLAST constant region database selection and rearrangement summary table showing the top C gene match, IgHM in this case.  The NCBI C genes database is based on the the current NCBI human Reference Genome annotation.

A new version of IgBLAST (1.16.0) is here!

We’ve released a new version (1.16.0) of IgBLAST , the popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. Version 1.16.0 has three new improvements.

  1. Added the ability to extend the J gene alignment at 3’ the end of the region (Figure 1). This allows you to view the unaligned bases that otherwise would not be included because of low sequence similarity. IgBLAST_options

Figure 1. The new “extend alignment at the 3′ end” option on the IgBLAST web form. The command line option is ‘-extend_align3end’. Continue reading “A new version of IgBLAST (1.16.0) is here!” →

A new version of IgBLAST (1.15.0) is here!

IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin (IG) and T cell receptor (TCR) variable domain sequences. We’ve released a new version (1.15.0) of IgBLAST with four new improvements / bug fixes:

  1. Support for the new framework region 4 (FWR4) annotation feature in the standard alignment formats and AIRR format.
  2. Renamed the previous “-penalty” parameter to -V_penalty to be consistent with other IgBLAST penalty options.
  3. Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) so that this process is not influenced by user-provided parameters.
  4. Corrected FWR/CDR annotations for certain mouse VK and rat VH germline genes.

IgBLAST 1.15 is available for download from the BLAST FTP area. See the manual on GitHub for information about setting up and running IgBLAST.

IgBLAST 1.9.0 release includes AIRR rearrangement reporting

IgBLAST 1.9.0 supports the adaptive immune receptor repertoire (AIRR) standard for sequence analysis results. The AIRR format is available on web IgBLAST as well as in the standalone IgBLAST tool, with the -outfmt 19 option.

Supporting this new schema in IgBLAST will enhance the increasing amount of repertoire studies that use next-generation sequencing technology to generate very large sets of Ig/T-cell receptor rearrangement analysis data.

IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. Get IgBLAST on FTP. A new manual is on GitHub.

New releases from NCBI: IgBLAST 1.7.0 and Sequence Viewer 3.21

IgBLAST 1.7.0 release

A new version of IgBLAST is now available on FTP, with the following new features:

  1. Specify whether overlapping nucleotides at VDJ junctions are allowed in matching V, D, and J genes.
  2. Set a custom J gene mismatch penalty
  3. Report the CDR3 start and stop positions in the sub-region table
  4. Use alignment length instead of percent identity as the tie-breaker for hits with identical blast scores, improving accuracy in the V, D, J gene assignment.

IgBLAST was developed at the NCBI to facilitate the analysis of immunoglobulin and T cell receptor variable domain sequences.

Continue reading “New releases from NCBI: IgBLAST 1.7.0 and Sequence Viewer 3.21” →