<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/34493? https://bioinformaticsonline.com/bookmarks/view/41033/clark-fast-accurate-and-versatile-sequence-classification-system Sat, 15 Feb 2020 01:49:01 -0600 https://bioinformaticsonline.com/bookmarks/view/41033/clark-fast-accurate-and-versatile-sequence-classification-system <![CDATA[CLARK: Fast, accurate and versatile sequence classification system]]> CLARK, a method based on a supervised sequence classification using discriminative k-mers. Considering two distinct specific classification problems (see the article for details), namely (1) the taxonomic classification of metagenomic reads to known bacterial genomes, and (2) the assignment of BAC clones and transcript to chromosome arms/centromeres (in the absence of a finished assembly for the reference genome), CLARK outperforms in classification speed and precision the best state-of-the-art methods.

http://clark.cs.ucr.edu/Spaced/

Address of the bookmark: http://clark.cs.ucr.edu/Spaced/

]]> Jit https://bioinformaticsonline.com/bookmarks/view/44641/heliano-a-fast-and-accurate-tool-for-detection-of-helitron-like-elements Tue, 13 Aug 2024 07:16:34 -0500 https://bioinformaticsonline.com/bookmarks/view/44641/heliano-a-fast-and-accurate-tool-for-detection-of-helitron-like-elements <![CDATA[HELIANO: A fast and accurate tool for detection of Helitron-like elements]]> Helitron-like elements (HLE1 and HLE2) are DNA transposons. They have been found in diverse species and seem to play significant roles in the evolution of host genomes. Although known for over twenty years, Helitron sequences are still challenging to identify. Here, we propose HELIANO (Helitron-like elements annotator) as an efficient solution for detecting Helitron-like elements.

https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkae679/7730539?login=true

Address of the bookmark: https://github.com/Zhenlisme/heliano/

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing Mon, 06 Aug 2018 17:19:15 -0500 https://bioinformaticsonline.com/bookmarks/view/37496/gsearch-a-fast-and-flexible-general-search-tool-for-whole-genome-sequencing <![CDATA[gSearch: a fast and flexible general search tool for whole-genome sequencing]]> gSearch compares sequence variants in the Genome Variation Format (GVF) or Variant Call Format (VCF) with a pre-compiled annotation or with variants in other genomes. Its search algorithms are subsequently optimized and implemented in a multi-threaded manner. 

Address of the bookmark: http://ml.ssu.ac.kr/gSearch/index.html

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data Tue, 27 Nov 2018 04:43:57 -0600 https://bioinformaticsonline.com/bookmarks/view/38304/lordfast-sensitive-and-fast-alignment-search-tool-for-long-noisy-read-sequencing-data <![CDATA[lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data]]> lordFAST is a sensitive tool for mapping long reads with high error rates. lordFAST is specially designed for aligning reads from PacBio sequencing technology but provides the user the ability to change alignment parameters depending on the reads and application.

lordFAST, a novel long-read mapper that is specifically designed to align reads generated by PacBio and potentially other SMS technologies to a reference. lordFAST not only has higher sensitivity than the available alternatives, it is also among the fastest and has a very low memory footprint.

 

Address of the bookmark: https://github.com/vpc-ccg/lordfast

]]> BioJoker 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 https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs Fri, 26 Jul 2024 06:04:26 -0500 https://bioinformaticsonline.com/blog/view/44616/basics-of-blast-programs <![CDATA[Basics of BLAST Programs !]]> The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

]]> BioStar https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads Thu, 24 May 2018 08:33:26 -0500 https://bioinformaticsonline.com/bookmarks/view/36755/minialign-fast-and-accurate-alignment-tool-for-pacbio-and-nanopore-long-reads <![CDATA[minialign: fast and accurate alignment tool for PacBio and Nanopore long reads]]> Address of the bookmark: https://github.com/ocxtal/minialign

]]> Jit https://bioinformaticsonline.com/bookmarks/view/39213/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads Tue, 02 Apr 2019 21:54:55 -0500 https://bioinformaticsonline.com/bookmarks/view/39213/flye-fast-and-accurate-de-novo-assembler-for-single-molecule-sequencing-reads <![CDATA[Flye: Fast and accurate de novo assembler for single molecule sequencing reads]]> Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. It is designed for a wide range of datasets, from small bacterial projects to large mammalian-scale assemblies. The package represents a complete pipeline: it takes raw PB / ONT reads as input and outputs polished contigs. Flye also includes a special mode for metagenome assembly.

Address of the bookmark: https://github.com/fenderglass/Flye

]]> BioJoker 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

]]> LEGE https://bioinformaticsonline.com/bookmarks/view/43439/mmseqs2-ultra-fast-and-sensitive-sequence-search-and-clustering-suite Wed, 06 Oct 2021 07:01:14 -0500 https://bioinformaticsonline.com/bookmarks/view/43439/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

]]> Abhi