Research Article

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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
09/30/2008
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
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
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
08/07/2014
BLAST; Chloroplast loci; DNA barcoding; Nuclear DNA marker

Genuine medicinal plant materials are very important for potential crude drug production, which can be used to cure many human diseases. DNA barcoding of medicinal plants is an effective way to identify adulterated or contaminated market materials, but it can be quite challenging to generate barcodes and analyze the data to determine discrimination power. The molecular phylogeny of a ... more

F. Al-Qurainy; S. Khan; M. Nadeem; M. Tarroum; A. Al-Ameri
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
10/04/2007
Data integration; Databases; MySQL; Proteomics; Schistosoma; Transcriptomics

Proteomics correspond to the identification and quantitative analysis of proteins expressed in different conditions or life stages of a cell or organism. Methods used in proteomics analysis include mainly chromatography, two-dimensional electrophoresis and mass spectrometry. Data generated in proteomics analysis vary significantly, and to identify a protein it is often necessary to ... more

A.C. Faria-Campos; R.R. Gomes; F.S. Moratelli; H. Rausch-Fernandes; G.R. Franco; S.V.A. Campos