Tag: Immunoglobulin and T cell receptor BLAST (IgBLAST)
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.
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.
- 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.
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!” →
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:
- Support for the new framework region 4 (FWR4) annotation feature in the standard alignment formats and AIRR format.
- Renamed the previous “-penalty” parameter to -V_penalty to be consistent with other IgBLAST penalty options.
- Restored constant internal BLAST search parameters for domain annotation (i.e., FWR/CDR) so that this process is not influenced by user-provided parameters.
- 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 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 (1.14.0) of IgBLAST with three new improvements / bug fixes:
- Adaptive Immune Receptor Repertoire (AIRR) format is more consistent with AIRR specs including changing undefined type (NON, N/A) to empty string, not appending “reversed” to sequence identifier when the query is in reversed orientation, and using standard locus names such as IGH, TRB instead of traditional VH, VB etc.
- The logic for showing CDR3 end of TCR sequences is improved.
- The sequence identifier is restored in the case of no results in AIRR rearrangement format.
IgBLAST 1.14 is available for download from the BLAST FTP area. See the the new manual on GitHub for information about setting up and running IgBLAST.
IgBLAST is a popular NCBI package for classifying and analyzing immunoglobulin and T cell receptor variable domain sequences. We’ve released a new version of IgBLAST with three new improvements:
- The new release determines the V gene reading frame from the end of FWR3 region instead of end of V gene. This helps identify the correct reading frames for rearrangements that have insertions or deletions near the V gene end.
- The allowed distance between V gene end and J gene start has been increased to 225 bp to allow detection of ultra long D/N regions.
- The standalone program and files has been repackaged to make it easier to install.
The new release is available from the BLAST FTP area, along with a new manual on GitHub.
We’ve released a new version of IgBLAST, v1.12. This new version increases the 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.
IgBLAST 1.12 uses the 1-based sequence coordinate system that reflects the change in the new AIRR Rearrangement Schema. Also, it includes fixes for minor bugs found in previous versions.
The new executables are available on the NCBI FTP site.
For more information, please read:
IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
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.
A new version of IgBLAST is now available on FTP, along with a new manual on GitHub. This release has the following improvements:
- The igblastn executable can now multi-thread much more efficiently for large sets of queries. The default number of threads is now four, but can be changed with the -num_threads option.
- The igblastn executable can now take an SRA accession as the query input. The search runs on the local machine, but the queries are retrieved from the SRA repository at the NCBI. Use the -sra rather than the -query option to enable.
- A lower default nucleotide mismatch penalty values for finding D and J genes (from -4 to -2 and from -3 to -2, respectively). This improves accuracy in finding the best D and J gene hits for moderately mutated sequences.
Our web IgBLAST page also uses the new default nucleotide mismatch penalty values (i.e., -2 for finding both D and J genes).
IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
IgBLAST 1.7.0 release
A new version of IgBLAST is now available on FTP, with the following new features:
- Specify whether overlapping nucleotides at VDJ junctions are allowed in matching V, D, and J genes.
- Set a custom J gene mismatch penalty
- Report the CDR3 start and stop positions in the sub-region table
- 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” →