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Databases

This document provides summaries of several databases and tools available from the National Center for Biotechnology Information (NCBI). It describes databases containing influenza virus sequences and BLAST databases in various formats. It also summarizes several bioinformatics tools from NCBI, including BLAST, COBALT, CD Search and e-PCR, which are used for sequence alignment and analysis.

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46 views

Databases

This document provides summaries of several databases and tools available from the National Center for Biotechnology Information (NCBI). It describes databases containing influenza virus sequences and BLAST databases in various formats. It also summarizes several bioinformatics tools from NCBI, including BLAST, COBALT, CD Search and e-PCR, which are used for sequence alignment and analysis.

Uploaded by

dhanapal6sb
Copyright
© Attribution Non-Commercial (BY-NC)
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOCX, PDF, TXT or read online on Scribd
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Databases

Influenza Virus A compilation of data from the NIAID Influenza Genome Sequencing Project and GenBank. It provides tools for flu sequence analysis, annotation and submission to GenBank. This resource also has links to other flu sequence resources, and publications and general information about flu viruses.

Downloads
BLAST (Stand-alone) BLAST executables for local use are provided for Solaris, LINUX, Windows, and MacOSX systems. See the README file in the ftp directory for more information. Preformatted databases for BLAST nucleotide, protein, and translated searches also are available for downloading under the db subdirectory. FTP: BLAST Databases Sequence databases for use with the stand-alone BLAST programs. The files in this directory are pre-formatted databases that are ready to use with BLAST. FTP: FASTA BLAST Databases Sequence databases in FASTA format for use with the stand-alone BLAST programs. These databases must be formatted using formatdb before they can be used with BLAST. FTP: UniVec This site contains the UniVec and UniVec_Core databases in FASTA format. See the README.uv file for details.

Tools
BLAST Link (BLink) A link option on protein records that displays the results of a pre-computed BLAST search of that protein against all other protein sequences at NCBI. BLAST Microbial Genomes Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes. BLAST RefSeqGene

Performs a BLAST search of the genomic sequences in the RefSeqGene/LRG set. The default display provides ready navigation to review alignments in the Graphics display. Basic Local Alignment Search Tool (BLAST) Finds regions of local similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as to help identify members of gene families. COBALT COBALT is a protein multiple sequence alignment tool that finds a collection of pairwise constraints derived from conserved domain database, protein motif database, and sequence similarity, using RPS-BLAST, BLASTP, and PHI-BLAST. Concise Microbial Protein BLAST A specialized BLAST service in which the queried database consists of all proteins from complete microbial (prokaryotic) genomes. NCBI has precalculated clusters of similar proteins at the genus-level and one representative is chosen from each cluster in order to reduce the dataset, thereby reducing search time and providing a broader taxonomic view. Conserved Domain Search Service (CD Search) Identifies the conserved domains present in a protein sequence. CD-Search uses RPSBLAST (Reverse Position-Specific BLAST) to compare a query sequence against position-specific score matrices that have been prepared from conserved domain alignments present in the Conserved Domain Database (CDD). Electronic PCR (e-PCR) A computational procedure that is used to identify sequence tagged sites (STSs) within DNA sequences. e-PCR looks for potential STSs in DNA sequences by searching for subsequences that closely match the PCR primers and have the correct order, orientation, and spacing that could represent the PCR primers used to generate known STSs.

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