<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/35131?offset=550 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/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/41442/gsp4pdb-a-web-tool-to-visualize-search-and-explore-protein-ligand-structural-patterns Sun, 15 Mar 2020 03:41:12 -0500 https://bioinformaticsonline.com/bookmarks/view/41442/gsp4pdb-a-web-tool-to-visualize-search-and-explore-protein-ligand-structural-patterns <![CDATA[GSP4PDB: a web tool to visualize, search and explore protein-ligand structural patterns]]> GSP4PDB is a user-friendly and efficient application to search and discover new patterns of protein-ligand interaction.

GSP4PDB is part of the services provided by the Bioinformatic Group of the University of Talca

http://gdblab.com/gsp4pdb/gsp4pdb2/

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-3352-x

Address of the bookmark: http://gdblab.com/gsp4pdb/gsp4pdb2/

]]> Neel https://bioinformaticsonline.com/bookmarks/view/44292/gget Sat, 01 Apr 2023 09:42:07 -0500 https://bioinformaticsonline.com/bookmarks/view/44292/gget <![CDATA[gget]]> gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.

image

Address of the bookmark: https://github.com/pachterlab/gget

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