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
09/30/2005
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
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
12/18/2014
Breeding; Conservation; Guava; Microsatellite markers; Morphological descriptors

The family Myrtaceae is widespread in the Atlantic Forest and is well-represented in the Espírito Santo State in Brazil. In the genus Psidium of this family, guava (Psidium guajava L.) is the most economically important species. Guava is widely cultivated in tropical and subtropical countries; however, the widespread cultivation of only a small number of guava tree ... more

A.M. Nogueira; M.F.S. Ferreira; J.H.S. Guilhen; A. Ferreira
09/09/2015
AFLP; Argopecten; Heterosis; Hybrid; SSR

Argopecten purpuratus and Argopecten irradians irradi­ans hybridization was successfully performed and the hybrid offspring displayed apparent heterosis in growth traits. To better understand the genetic basis of heterosis, the genomic composition and genetic varia­tion of the hybrids were analyzed with amplified fragment length poly­morphism (AFLP) and simple sequence repeat (SSR) ... more

L.P. Hu; X.T. Huang; Y. Sun; J.X. Mao; S. Wang; C.D. Wang; Z.M. Bao
07/03/2015
Cerrado; Enrichment genomic library; Mangaba; SSR; STR

Herein, we describe 34 microsatellite loci developed using an enrichment genomic library for the tree species Hancornia speciosa Gomes (Apocynaceae). Thirty-five individuals were genotyped using 34 primers to analyze the polymorphisms at each locus. The number of alleles per locus ranged from 4 to 20. The average number of alleles was 8.11, and the expected heterozygosity ranged from ... more

A.J.L. Rodrigues; A.T. Yamaguishi; L.J. Chaves; A.S.G. Coelho; J.S. Lima; M.P.C. Telles

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