NCBI-BLAST

J-Similarity S Homology Blast2 ASD HEW Blast -EVEC Blast2 NCBI Blast Parasite Blast2 -WU Fasta... 

Specifically degree of identical sequence alignment based on NCBI Blast 2 comparisons bBased on the predicted chimpanzee dysbindin-IA (XP 001169961 in NCBI database)... 

Because of the many factors on which BLAST scores and statistics depend, the results of disparate searches may not be directly compared. To standardize across scoring schemes and variable database composition, the formula B = (kx - In K)l (In 2) is used to convert an alignment score x into a bit score B. This conversion effectively removes K and X from subsequent calculations, standardizing all BLAST searches to reference the same EVD. It is the bit score which NCBI-BLAST includes along with the / -value of each reported high-scoring local alignment. We demonstrate in the next section with an example. 

The most popular tool currently in use is BLAST (Basic Local Alignment Search Tool) (3 7) from the NCBI. BLAST is an example of a heuristic that attempts to optimize a specific similarity measure. The most recent revisions to the algorithm are gapped BLAST and PSI-BLAST (38), with improved accuracy for PSI-BLAST using composition-based statistics... 

Key Words NCBI BLAST mini-courses MegaBLAST human genome. 

Since this chapter was sent for publication the NCBI BLAST site has undergone a major revampling. In the new system the values entered by the user are retained in memory . The user can also access multiple old results and reformat or rerun the same search by changing parameters. It is suggested that the readers familiarize themselves with the new front-end, before attempting further experiments along the lines suggested in this chapter. 

Optional software. Some advanced analysis steps (Subheadings 3.6.8. and 3.6.10.) require additional software to be installed on the system. To create HTML formatted output of the results as described in Subheading 3.6.8., the Vienna RNA package (www.tbi.univie.ac.at/RNA) and the postscript interpreter Ghostscript (http //www.cs.wisc.edu/ ghost/) need to be installed. To perform automatic database searches of predicted ncRNA candidates the user will need NCBI Blast (ftp //ftp.ncbi.nih.gov/blast). 

We cannot cover in detail the installation procedure of the optional software. We will just give an outline of how to install the Vienna RNA package and NCBI blast on a standard Linux system. Together with an existing Ghostscript installation, this will allow the examples to be run in Subheadings 3.6.8. and 3.6.10. for Windows and OS X (see Note 3). 

To install NCBI Blast, download the blast-2.. tar.gz-package matching the platform from ftp //ftp.ncbi.nih.gov/blast/executables/LATEST/. Copy it to the installation directory of choice and untar it. The executables are located in the bin subdirectory, which should be added to the PATH variable. 

To install NCBI blast on windows, create a new folder (e.g., c Program Files blast) and download the blast-2. -win32.exe file from ftp //ftp.ncbi.nih.gov/ blast. Within the new folder, double click on the blast-2. - Win32. exe file, which extracts the programs and data. Add the bin subdirectory to the Path right-click My computer , then click Properties . Select Advanced/ Environment variables/New . Add the complete path of the blast bin directory to the variable Path, use as separator. 

Assigning Function by Direct Sequence Similarity NCBI-BLAST (http //www.ncbi.nlm.nih.gov/BLAST/)... 

Sequence analysis. The GenBank database was searched using the NCBI BLAST program. Consensus sequences were generated and analysed using the programs of the DNASTAR. Multiple alignments of nucleotide were performed with the Clustal... 

Figure 8.10. Database similarity search on the World Wide Web. The figure illustrates the use of the NCBI BLAST Web front end. The query sequence should be pasted from the clipboard into the large text field (where the sequence of U43746 is shown in this figure). Other essential elements of the search are the name of the search program and the database, both of which may be selected from drop-down lists. Additional optional parameters may be set if desired. In addition to this "Advanced BLAST" form, there is also a "Basic BLAST" form in which the advanced options are hidden. In either case, simply press the Submit Query button to begin the search.

Nominal naa> (M,) i 71317 Calculated pi value 9.92 NCBI BLAST laacoh of albh wnHm agaicat nr... 

Graphical rich information is cross-linked via iframes. Iframes are transparent windows within an HTML page and allow the display of information from one server into an HTML page of another server (here the Harvester pages) in real time. Several of those iframes are combined on every individual Harvester page. The information displayed via these iframes is therefore always up to date. Currently Harvester has implemented six servers via iframes (NCBI BLAST, Genome-Browser, Ensembl, RZPD, CD ART, STRING). 

Navigate with your browser to The National Center for Biotechnology Information (NCBI) BLAST website http //blast.ncbi.nlm.nih.gov/Blast.cgi. Figure 4.11 shows the NCBI BLAST Home page. 

Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL. NCBI BLAST a better web interface. Nucleic Acids Res 2008 36(Suppl 2) W5-W9. 

NCBI BLAST is the Basic Local Alignment Search Tool (BLAST) by the National Center for Biotechnology Information (Altschul et al. 1990). 

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