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Database resources of the National Center for Biotechnology Information

by David L. Wheeler, Tanya Barrett, Dennis A. Benson, Stephen H. Bryant, Kathi Canese, Vyacheslav Chetvernin, Deanna M. Church, Michael Dicuccio, Ron Edgar, Scott Federhen, Lewis Y. Geer, Yuri Kapustin, Oleg Khovayko, David L, David J. Lipman, Thomas L. Madden, Donna R. Maglott, James Ostell, Vadim Miller, Kim D. Pruitt, Gregory D. Schuler, Edwin Sequeira, Steven T. Sherry, Karl Sirotkin, Re Souvorov, Grigory Starchenko, Roman L. Tatusov, Tatiana A. Tatusova, Lukas Wagner, Eugene Yaschenko - Nucleic Acids Res , 2008
"... In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez, ..."
Abstract - Cited by 964 (15 self) - Add to MetaCart
In addition to maintaining the GenBankÒ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s Web site. NCBI resources include Entrez,

Pfam protein families database

by Robert D. Finn, John Tate, Jaina Mistry, Penny C. Coggill, Stephen John Sammut, Hans-rudolf Hotz, Goran Ceric, Kristoffer Forslund, Sean R. Eddy, Erik L. L. Sonnhammer, Alex Bateman - Nucleic Acids Research, 2008, 36(Database issue): D281–D288
"... Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI GenP ..."
Abstract - Cited by 748 (13 self) - Add to MetaCart
Pfam is a comprehensive collection of protein domains and families, represented as multiple sequence alignments and as profile hidden Markov models. The current release of Pfam (22.0) contains 9318 protein families. Pfam is now based not only on the UniProtKB sequence database, but also on NCBI Gen

2005 MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res

by Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, Takashi Miyata
"... The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement opti-ons, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed hig ..."
Abstract - Cited by 788 (5 self) - Add to MetaCart
database. Such improvement was gen-erally observed for most methods, but remarkably large for the new options of MAFFT proposed here. Thus, we made a Ruby script, mafftE.rb, which aligns the input sequences together with their close homo-logues collected from SwissProt using NCBI-BLAST.

NCBI reference sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

by Kim D. Pruitt, Tatiana Tatusova, Donna R. Maglott - Nucleic Acids Res , 2005
"... transcripts and proteins ..."
Abstract - Cited by 586 (6 self) - Add to MetaCart
transcripts and proteins

Mfold web server for nucleic acid folding and hybridization prediction

by Michael Zuker - Nucleic Acids Res , 2003
"... The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding ..."
Abstract - Cited by 1955 (0 self) - Add to MetaCart
The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding

Multiple sequence alignment with the Clustal series of programs

by Ramu Chenna, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie D. Thompson - Nucleic Acids Res , 2003
"... The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the ..."
Abstract - Cited by 725 (5 self) - Add to MetaCart
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also

Biological sequence analysis: probabilistic models of proteins and nucleic acids

by Richard Durbin, Sean Eddy, Anders Krogh, Graeme Mitchison , 1998
"... ..."
Abstract - Cited by 1191 (21 self) - Add to MetaCart
Abstract not found

The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000

by Amos Bairoch, Rolf Apweiler - Nucleic Acids Res , 2000
"... SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with othe ..."
Abstract - Cited by 761 (21 self) - Add to MetaCart
SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

by Jimmy K. Eng, Ashley L. Mccormack, John R. Yates - J. Am. Soc. Mass Spectrom , 1994
"... A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (lo-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a mas ..."
Abstract - Cited by 936 (18 self) - Add to MetaCart
A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (lo-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a

Gapped Blast and PsiBlast: a new generation of protein database search programs

by Stephen F. Altschul, Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, David J. Lipman - NUCLEIC ACIDS RESEARCH , 1997
"... The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while ..."
Abstract - Cited by 8393 (85 self) - Add to MetaCart
The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased substantially while
Results 1 - 10 of 314,503