Fast semi-local alignment for DNA sequence database search

2003 ◽  
Author(s):  
Yong-Sheng Chen ◽  
Yi-Ping Hung ◽  
Chiou-Shann Fuh
Keyword(s):  
Dna Sequence ◽  
Database Search ◽  
Local Alignment ◽  
Sequence Database ◽  
Sequence Database Search

scholarly journals A Tandem Mass Spectrometry Sequence Database Search Method for Identification of O-Fucosylated Proteins by Mass Spectrometry

2018 ◽  
Vol 18 (2) ◽  
pp. 652-663 ◽  
Author(s):  
Kristian E. Swearingen ◽  
Jimmy K. Eng ◽  
David Shteynberg ◽  
Vladimir Vigdorovich ◽  
Timothy A. Springer ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Tandem Mass Spectrometry ◽  
Database Search ◽  
Search Method ◽  
Tandem Mass ◽  
Sequence Database ◽  
Sequence Database Search

Human plasma proteome analysis by reversed sequence database search and molecular weight correlation based on a bacterial proteome analysis

PROTEOMICS ◽  
2006 ◽  
Vol 6 (4) ◽  
pp. 1121-1132 ◽  
Author(s):  
Gun Wook Park ◽  
Kyung-Hoon Kwon ◽  
Jin Young Kim ◽  
Jeong Hwa Lee ◽  
Sung-Ho Yun ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Human Plasma ◽  
Proteome Analysis ◽  
Database Search ◽  
Plasma Proteome ◽  
Sequence Database ◽  
Sequence Database Search ◽  
Human Plasma Proteome

Comet: An open-source MS/MS sequence database search tool

PROTEOMICS ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 22-24 ◽  
Author(s):  
Jimmy K. Eng ◽  
Tahmina A. Jahan ◽  
Michael R. Hoopmann
Keyword(s):  
Open Source ◽  
Database Search ◽  
Sequence Database ◽  
Search Tool ◽  
Sequence Database Search

The disconnect between DNA and species names: lessons from reptile species in the NCBI taxonomy database

Zootaxa ◽  
2019 ◽  
Vol 4706 (3) ◽  
pp. 401-407 ◽  
Author(s):  
AKHIL GARG ◽  
DETLEF LEIPE ◽  
PETER UETZ
Keyword(s):  
Dna Sequence ◽  
Dna Sequences ◽  
Ncbi Taxonomy ◽  
Sequence Database ◽  
Ncbi Taxonomy Database ◽  
Reptile Species

We compared the species names in the Reptile Database, a dedicated taxonomy database, with those in the NCBI taxonomy database, which provides the taxonomic backbone for the GenBank sequence database. About 67% of the known ~11,000 reptile species are represented with at least one DNA sequence and a binary species name in GenBank. However, a common problem arises through the submission of preliminary species names (such as “Pelomedusa sp. A CK-2014”) to GenBank and thus the NCBI taxonomy. These names cannot be assigned to any accepted species names and thus create a disconnect between DNA sequences and species. While these names of unknown taxonomic meaning sometimes get updated, often they remain in GenBank which now contains sequences from ~1,300 such “putative” reptile species tagged by informal names (~15% of its reptile names). We estimate that NCBI/GenBank probably contain tens of thousands of such “disconnected” entries. We encourage sequence submitters to update informal species names after they have been published, otherwise the disconnect will cause increasing confusion and possibly misleading taxonomic conclusions.

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