Research Article

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09/30/2008
Annotation; BLAST; Expressed sequence tags; KEGG Orthology; orthologs

The KEGG Orthology (KO) database was tested as a source for automated annotation of expressed sequence tags (ESTs). We used a control experiment where every EST was assigned to its cognate protein, and an annotation experiment where the ESTs were annotated by proteins from other organisms. Analyzing the results, we could assign classes to the annotation: correct, changed and speculated. The ... more

G.R. Fernandes; M.A. Mudado; J.M. Ortega
11/27/2014
BLAST; Blast resistance; QTL mapping; Recombinant inbred lines; Rice

Bodao, a japonica landrace from the Taihu Lake region of China, is highly resistant to most Chinese isolates of Magnaporthe oryzea, a form of rice blast. To effectively dissect the influence of genetics on this blast resistance, a population of 155 recombinant inbred lines (F2:8) derived from a cross of Bodao x Suyunuo was inoculated with 12 blast isolates. ... more

J. Huan; Y.M. Bao; Y.Y. Wu; G.Y. Zeng; W.W. He; L.L. Dang; J.F. Wang; H.S. Zhang
02/21/2014
Chloroplast loci; DNA barcode; Endemic plant; Nepetalactone

Molecular markers, mainly DNA-based are potential tools for DNA barcoding and phylogenetic study. The plant species belonging to the Nepeta genus have important medicinal value because of the presence of nepetalactones, and they have been used to treat human diseases. We amplified nuclear and chloroplast gene loci to develop a DNA barcode and phylogenetic study of Nepeta ... more

F. Al-Qurainy; S. Khan; M. Nadeem; M. Tarroum; A.R.Z. Gaafar
12/30/2004
BLAST; DNA sequence quality; PHRED; Quality window; SAGE

When analyzing sequencing reads, it is important to distinguish between putative correct and wrong bases. An open question is how a PHRED quality value is capable of identifying the miscalled bases and if there is a quality cutoff that allows mapping of most errors. Considering the fact that a low quality value does not necessarily indicate a miscalled position, we decided to ... more

F. Prosdocimi; F.Cruz Peixoto; J.Miguel Ortega
09/30/2005
BLAST; Databases; Driver

There are many bioinformatics tools that deal with input/output (I/O) issues by using filing systems from the most common operating systems, such as Linux or MS Windows. However, as data volumes increase, there is a need for more efficient disk access, ad hoc memory management and specific page-replacement policies. We propose a device driver that can be used by multiple ... more

R.Campos Mauro; S. Lifschitz
03/11/2013
BLAST; Conservation measures; nrDNA; Rare species

The rare and endangered plants of any country are important genetic resources that often require urgent conservation measures. Assessment of phylogenetic relationships and evaluation of genetic diversity is very important prior to implementation of conservation strategies for saving rare and endangered plant species. We used internal transcribed spacer sequences of nuclear ribosomal DNA ... more

F. Al-Qurainy; S. Khan; M. Nadeem; M. Tarroum; A. Alaklabi
10/14/2017
Anacardium occidentale; BLAST; Cashew; DNA fingerprinting; ITS region; PCR; extraction DNA

This study performed a genetic study of several canopies of Anacardium occidentale L. specimen called "Cashew King" (Cajueiro da Praia-PI, Brazil) in order to assess whether all canopies belong to the same plant. Leaves were collected from  different distant points, and preserved for analysis of DNA. The analysis was made from automated sequencing by capillary ... more

F.P.M. do Amaral; G.H. de Sa; L.A. Filgueiras; F.S.Santos Filho; C.J.R.Santos Soares; M.P.M. do Amaral; S.E. dos Sant Valente; A.N. Mendes
12/28/2021
BLAST; Guava; Identity; SSR

BLAST is a genomic local alignment search tool used to identify homology between genotypes and possible orthologous genes. In vitro microsatellite transferability is a strategy to enable or increase species molecular fingerprinting, but it is dependent on PCR technique. An initial in silico step using BLAST for transferability can be helpful to ... more

F.L.B. Medeiros; C.A.F. Santos; A.E.S. Costa
05/25/2022
BLAST; Eucalyptus; Guava; SNPs transferability

Genome mapping is a simplified representation of molecular markers or nucleotide sequences in chromosomes; developing accurate and dense maps is crucial for marker-assisted selection. We developed and compared genetic linkage maps obtained using JoinMap 4.0 and GACD with a physical map obtained using BLAST analysis based on Eucalyptus SNPs transferred to ... more

F.L.B. Medeiros; C.A.F. Santos; A.E.S. Costa
10/26/2011
COI; Cytochrome oxidase I; DNA barcoding; European bee-eater; Green bee-eater; Phylogenetics

DNA barcoding using mitochondrial cytochrome c oxidase subunit I (COI) is regarded as a standard method for species identification. Recent reports have also shown extended applications of COI gene analysis in phylogeny and molecular diversity studies. The bee-eaters are a group of near passerine birds in the family Meropidae. There are 26 species worldwide; five of them are found in Saudi ... more

I.A. Arif; H.A. Khan; M. Shobrak; J. Williams

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