<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/44589?offset=80 https://bioinformaticsonline.com/news/view/44370/ncbiblast-2141-now-available Wed, 30 Aug 2023 02:36:13 -0500 https://bioinformaticsonline.com/news/view/44370/ncbiblast-2141-now-available <![CDATA[NCBIBLAST+ 2.14.1 now available]]> #NCBIBLAST+ 2.14.1 now available with improved documentation, faster and more reliable database downloads, and some bug fixes. 

Check out the changes they made.

They added the cleanup-blastdb-volumes.py script to remove unused BLAST database volumes. Read the documentation here.

They also switched the protocol from ftp to https to access BLAST databases for increased performance and reliability when downloading data from the NCBI with the update_blastdb.pl script.

And fixed a few bugs related to downloading data from the NCBI, and mt_mode crashing blastn and blastx.

Check out the release notes.

Download BLAST+ 2.14.1

Questions or comments? Please write the BLAST help desk.

More info and download: https://blast.ncbi.nlm.nih.gov/doc/blast-news/2023-BLAST-News.html

]]> Neel https://bioinformaticsonline.com/bookmarks/view/35131/giggle-a-search-engine-for-large-scale-integrated-genome-analysis Wed, 10 Jan 2018 03:10:45 -0600 https://bioinformaticsonline.com/bookmarks/view/35131/giggle-a-search-engine-for-large-scale-integrated-genome-analysis <![CDATA[GIGGLE: a search engine for large-scale integrated genome analysis]]> GIGGLE is a genomics search engine that identifies and ranks the significance of genomic loci shared between query features and thousands of genome interval files. GIGGLE (https://github.com/ryanlayer/giggle) scales to billions of intervals and is over three orders of magnitude faster than existing methods. Its speed extends the accessibility and utility of resources such as ENCODE, Roadmap Epigenomics, and GTEx by facilitating data integration and hypothesis generation.

https://www.nature.com/articles/nmeth.4556

Address of the bookmark: https://github.com/ryanlayer/giggle

]]> Jit https://bioinformaticsonline.com/bookmarks/view/42645/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Mon, 18 Jan 2021 10:47:56 -0600 https://bioinformaticsonline.com/bookmarks/view/42645/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite <![CDATA[MMseqs2: ultra fast and sensitive sequence search and clustering suite]]> MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source GPL-licensed software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.

Address of the bookmark: https://github.com/soedinglab/MMseqs2

]]> Manisha Mishra