A5064872013- Genomics and Phylogenetic Studies
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- Biomedical Text Mining and Ontologies
- RNA modifications and cancer
- Algorithms and Data Compression
- Library Science and Administration
- Rheology and Fluid Dynamics Studies
- Microfluidic and Capillary Electrophoresis Applications
- Molecular Biology Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Scientific Computing and Data Management
- Misinformation and Its Impacts
- Web and Library Services
- Microbial Community Ecology and Physiology
- American Environmental and Regional History
- Socioeconomic Development in Asia
- Monoclonal and Polyclonal Antibodies Research
- Dispute Resolution and Class Actions
- Hybrid Renewable Energy Systems
- CRISPR and Genetic Engineering
- Library Science and Information Literacy
- Advanced battery technologies research
National Institutes of Health
2009-2023
National Center for Biotechnology Information
2010-2023
Lockheed Martin (United States)
2015
Medical University of Graz
2009-2011
University of California, Santa Cruz
1989-1991
Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed current BLAST software suboptimal for long queries or database sequences. There are also some shortcomings in user-interface command-line applications.We describe features and improvements rewritten introduce new applications. Long query sequences broken into chunks processing, cases leading to dramatically...
Choosing appropriate primers is probably the single most important factor affecting polymerase chain reaction (PCR). Specific amplification of intended target requires that do not have matches to other targets in certain orientations and within distances allow undesired amplification. The process designing specific typically involves two stages. First, flanking regions interest are generated either manually or using software tools; then they searched against an nucleotide sequence database...
Basic Local Alignment Search Tool (BLAST) is a sequence similarity search program. The public interface of BLAST, http://www.ncbi.nlm.nih.gov/blast, at the NCBI website has recently been reengineered to improve usability and performance. Key new features include simplified forms, improved navigation, list recent BLAST results, saved strategies documentation directory. Here, we describe web application's features, explain design decisions outline plans for future improvement.
Basic Local Alignment Search Tool (BLAST) is one of the most heavily used sequence analysis tools available in public domain. There now a wide choice BLAST algorithms that can be to search many different databases via web pages (http://www.ncbi.nlm.nih.gov/BLAST/). All algorithm-database combinations executed with default parameters or customized settings, and results viewed variety ways. A new online resource, Program Selection Guide, has been created assist definition strategies. This...
'BLAST 2 Sequences', a new BLAST-based tool for aligning two protein or nucleotide sequences, is described. While the standard BLAST program widely used to search homologous sequences in and databases, one often needs compare only that are already known be homologous, coming from related species or, e.g. different isolates of same virus. In such cases searching entire database would unnecessarily time-consuming. Sequences' utilizes algorithm pairwise DNA-DNA protein-protein sequence...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published life science journals. Entrez system search retrieval operations most these data from 39 distinct databases. E-utilities serve as programming interface system. Augmenting many Web applications are custom implementations BLAST program optimized to specialized sets. New...
The Basic Local Alignment Search Tool (BLAST) website at the National Center for Biotechnology (NCBI) is an important resource searching and aligning sequences.A new BLAST report allows faster loading of alignments, adds navigation aids, easy downloading subject sequences reports has improved usability.Here, we describe these improvements to report, discuss design decisions, other search page database documentation outline plans future development.
Abstract Motivation: The BLAST software package for sequence comparison speeds up homology search by preprocessing a query into lookup table. Numerous research studies have suggested that the database instead would give better performance. However, production usage of methods preprocess has been limited to programs such as BLAT and SSAHA are designed find matches when subsequences highly similar. Results: We developed new version MegaBLAST module does initial phase finding short seeds...
The variable domain of an immunoglobulin (IG) sequence is encoded by multiple genes, including the (V) gene, diversity (D) gene and joining (J) gene. Analysis IG sequences typically requires identification each as well a comparison variations in context defined regions. General purpose tools, such BLAST program, have only limited use for tasks, rearranged nature length rounds searches single sequence. Additionally, manual assembly different genes difficult error-prone. To address these...
In addition to maintaining the GenBank(R) nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological available through NCBI's web site. NCBI include Entrez, Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Gene, Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Genome, Genome...
BLAST is a commonly-used software package for comparing query sequence to database of known sequences; in this study, we focus on protein sequences. Position-specific-iterated (PSI-BLAST) iteratively searches database, using the matches round i construct position-specific score matrix (PSSM) searching + 1. Biegert and Söding developed Context-sensitive (CS-BLAST), which combines information from with derived library short profiles achieve better homology detection than PSI-BLAST, builds its...
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI web site. include Entrez, Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Genomes...
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI's Web site. NCBI include Entrez, Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Gene, Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Genome,...
Basic local alignment search tool (BLAST) is a sequence similarity program. The National Center for Biotechnology Information (NCBI) maintains BLAST server with home page at http://www.ncbi.nlm.nih.gov/BLAST/ . We report here on recent enhancements to the results produced by NCBI. These include features highlight mismatches between similar sequences, show where query was masked low-complexity sequence, and integrate information about database sequences from NCBI Entrez system into display....
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI Web site. include Entrez, Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP,...
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI web site. include Entrez, Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Gene, Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes,...
In addition to maintaining the GenBank® nucleic acid sequence database, National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources data in GenBank other biological made available through NCBI Website. include Entrez, Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome related tools,...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published in life science journals. Entrez system search retrieval operations most these data from 38 distinct databases. E-utilities serve as programming interface system. Augmenting many web applications are custom implementations BLAST program optimized to specialized sets. New...
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources biological information and data, including the GenBank® nucleic acid sequence database PubMed citations abstracts published in life science journals. Entrez system search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface system. Custom implementations BLAST program provide sequence-based searching many specialized datasets. New released...
The National Center for Biotechnology Information (NCBI) provides online information resources biology, including the GenBank® nucleic acid sequence database and PubMed® of citations abstracts published in life science journals. NCBI search retrieval operations most these data from 35 distinct databases. E-utilities serve as programming interface New include Comparative Genome Resource (CGR) BLAST ClusteredNR database. Resources receiving significant updates past year PubMed, PMC, Bookshelf,...
Next-generation sequencing technologies can produce tens of millions reads, often paired-end, from transcripts or genomes. But few programs align RNA on the genome and accurately discover introns, especially with long reads. We introduce Magic-BLAST, a new aligner based ideas Magic pipeline.Magic-BLAST uses innovative techniques that include optimization spliced alignment score selective masking during seed selection. evaluate performance Magic-BLAST to map short sequences its ability...
Biomedical researchers use alignments produced by BLAST (Basic Local Alignment Search Tool) to categorize their query sequences. Producing such is an essential bioinformatics task that well suited for the cloud. The cloud can perform many calculations quickly as store and access large volumes of data. Bioinformaticians also it collaborate with other researchers, sharing results, datasets even pipelines on a common platform.We present ElasticBLAST, native application in ElasticBLAST handle...