<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/38670?offset=490 https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences Sun, 01 Nov 2020 16:52:58 -0600 https://bioinformaticsonline.com/news/view/42296/igblast-117-is-now-available-with-improved-identification-of-productive-v-gene-sequences <![CDATA[IgBLAST 1.17 is now available with improved identification of productive V gene sequences]]> A new release of IgBLAST (1.17), the popular package for classifying and analyzing immunoglobulin and T cell receptor sequences, is now available on the web and from the FTP site. The updated package is better at identifying productive V gene sequences. We added a new field , “V frame shift”, to the IgBLAST output to indicate whether the V gene translation frame contains a frame-shift. We have also updated the definition of a productive V(D)J sequence to now exclude those with internal frame shifts.

See the new IgBLAST manual on the NCBI GitHub site for more information on setting up and running IgBLAST.

If you have any questions or concerns, please email us at blast-help@ncbi.nlm.nih.gov

 

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify Tue, 05 Mar 2024 00:23:49 -0600 https://bioinformaticsonline.com/bookmarks/view/44479/doubletrouble-identify-duplicated-genes-from-whole-genome-protein-sequences-and-classify <![CDATA[doubletrouble: identify duplicated genes from whole-genome protein sequences and classify]]> doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

Address of the bookmark: https://bioconductor.org/packages/release/bioc/html/doubletrouble.html

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/44896/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences Sun, 31 Aug 2025 06:30:16 -0500 https://bioinformaticsonline.com/bookmarks/view/44896/jaeger-an-accurate-and-fast-deep-learning-tool-to-detect-bacteriophage-sequences <![CDATA[Jaeger : an accurate and fast deep-learning tool to detect bacteriophage sequences]]> Jaeger is a tool that utilizes homology-free machine learning to identify phage genome sequences that are hidden within metagenomes. It is capable of detecting both phages and prophages within metagenomic assemblies.

Address of the bookmark: https://github.com/MGXlab/Jaeger

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