Go to the SVN repository for this file.
49 "Stephen F. Altschul, Thomas L. Madden, \ 50 Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. \ 51 Lipman (1997), \"Gapped BLAST and PSI-BLAST: a new generation of protein \ 52 database search programs\", Nucleic Acids Res. 25:3389-3402.",
54 "Zheng Zhang, Alejandro A. Schäffer, Webb Miller, \ 55 Thomas L. Madden, David J. Lipman, Eugene V. Koonin, and Stephen F. \ 56 Altschul (1998), \"Protein sequence similarity searches using patterns \ 57 as seeds\", Nucleic Acids Res. 26:3986-3990.",
59 "Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), \ 60 \"A greedy algorithm for aligning DNA sequences\", \ 61 J Comput Biol 2000; 7(1-2):203-14.",
63 "Alejandro A. Schäffer, L. Aravind, Thomas L. Madden, Sergei Shavirin, \ 64 John L. Spouge, Yuri I. Wolf, Eugene V. Koonin, and Stephen F. Altschul \ 65 (2001), \"Improving the accuracy of PSI-BLAST protein database searches \ 66 with composition-based statistics and other refinements\", Nucleic Acids \ 69 "Stephen F. Altschul, John C. Wootton, E. Michael Gertz, Richa Agarwala, \ 70 Aleksandr Morgulis, Alejandro A. Schäffer, and Yi-Kuo Yu (2005) \"Protein \ 71 database searches using compositionally adjusted substitution matrices\", \ 72 FEBS J. 272:5101-5109.",
74 "Aleksandr Morgulis, George Coulouris, Yan Raytselis, \ 75 Thomas L. Madden, Richa Agarwala, Alejandro A. Schäffer \ 76 (2008), \"Database Indexing for Production MegaBLAST Searches\", \ 77 Bioinformatics 24:1757-1764.",
79 "Grzegorz M. Boratyn, Alejandro A. Schaffer, Richa Agarwala, Stephen F. Altschul, \ 80 David J. Lipman and Thomas L. Madden (2012) \"Domain enhanced lookup time \ 81 accelerated BLAST\", Biology Direct 7:12.",
89 "//www.ncbi.nlm.nih.gov/\ 90 entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9254694&dopt=Citation",
92 "//www.ncbi.nlm.nih.gov/\ 93 entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=9705509&dopt=Citation",
95 "//www.ncbi.nlm.nih.gov/\ 96 entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=10890397&dopt=Citation",
98 "//www.ncbi.nlm.nih.gov/\ 99 entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=11452024&dopt=Citation",
101 "//www.ncbi.nlm.nih.gov/\ 102 entrez/query.fcgi?db=PubMed&cmd=Retrieve&list_uids=16218944&dopt=Citation",
104 "//www.ncbi.nlm.nih.gov/pubmed/18567917",
106 "//www.ncbi.nlm.nih.gov/pubmed/22510480",
121string::size_type
offset= pub_string.find(
"ä");
122 if(
offset!= string::npos)
123pub_string.replace(
offset, 6,
"a");
Declares singleton objects to store the version and reference for the BLAST engine.
Function calls to actually perform a BLAST search (high level).
Class to keep track of the various BLAST references.
static string GetString(EPublication pub)
Reference for requested publication.
EPublication
Enumerates the various BLAST publications.
static string GetHTMLFreeString(EPublication pub)
Reference for requested publication without umlaut.
static const string kReferences[(int) CReference::eMaxPublications+1]
References for the various BLAST publications.
static const string kPubMedUrls[(int) CReference::eMaxPublications+1]
Pubmed URLs to retrieve the references defined above.
static string GetPubmedUrl(EPublication pub)
Get Pubmed url for requested publication.
@ eMaxPublications
Used as sentinel value.
#define END_NCBI_SCOPE
End previously defined NCBI scope.
#define END_SCOPE(ns)
End the previously defined scope.
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
#define BEGIN_SCOPE(ns)
Define a new scope.
unsigned int
A callback function used to compare two keys in a database.
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