Protein domain identification and improved sequence similarity searching using PSI-BLAST

2002 ◽  
Vol 48 (4) ◽  
pp. 672-681 ◽  
Author(s):  
Richard A. George ◽  
Jaap Heringa
Keyword(s):  
Sequence Similarity ◽  
Protein Domain ◽  
Similarity Searching ◽  
Domain Identification

A Similarity Searching System for Biological Phenotype Images Using Deep Convolutional Encoder-decoder Architecture

2019 ◽  
Vol 14 (7) ◽  
pp. 628-639 ◽  
Author(s):  
Bizhi Wu ◽  
Hangxiao Zhang ◽  
Limei Lin ◽  
Huiyuan Wang ◽  
Yubang Gao ◽  
...  
Keyword(s):  
Neural Network ◽  
Retrieval System ◽  
Sequence Similarity ◽  
Local Alignment ◽  
Similarity Searching ◽  
Loss Of Function ◽  
Biological Images ◽  
The Neural Network ◽  
Convolutional Autoencoder ◽  
Biological Phenotype

Background: The BLAST (Basic Local Alignment Search Tool) algorithm has been widely used for sequence similarity searching. Analogously, the public phenotype images must be efficiently retrieved using biological images as queries and identify the phenotype with high similarity. Due to the accumulation of genotype-phenotype-mapping data, a system of searching for similar phenotypes is not available due to the bottleneck of image processing. Objective: In this study, we focus on the identification of similar query phenotypic images by searching the biological phenotype database, including information about loss-of-function and gain-of-function. Methods: We propose a deep convolutional autoencoder architecture to segment the biological phenotypic images and develop a phenotype retrieval system to enable a better understanding of genotype–phenotype correlation. Results: This study shows how deep convolutional autoencoder architecture can be trained on images from biological phenotypes to achieve state-of-the-art performance in a phenotypic images retrieval system. Conclusion: Taken together, the phenotype analysis system can provide further information on the correlation between genotype and phenotype. Additionally, it is obvious that the neural network model of image segmentation and the phenotype retrieval system is equally suitable for any species, which has enough phenotype images to train the neural network.

scholarly journals Query-seeded iterative sequence similarity searching improves selectivity 5–20-fold

2016 ◽  
Vol 45 (7) ◽  
pp. e46-e46 ◽  
Author(s):  
William R. Pearson ◽  
Weizhong Li ◽  
Rodrigo Lopez
Keyword(s):  
Sequence Similarity ◽  
Iterative Sequence ◽  
Similarity Searching

scholarly journals EDITORIAL Beyond sequence similarity – the curious case of GW/WG protein domain

2011 ◽  
Vol 4 ◽  
pp. 303-305
Author(s):  
Wojciech M. Karlowski
Keyword(s):  
Sequence Similarity ◽  
Protein Domain

Sequence Similarity Searching

2018 ◽  
Vol 95 (1) ◽  
pp. e71 ◽  
Author(s):  
Gang Hu ◽  
Lukasz Kurgan
Keyword(s):  
Sequence Similarity ◽  
Similarity Searching

HACRE1, a recently inserted copia-like retrotransposon of sunflower (Helianthus annuus L.)

Genome ◽  
2009 ◽  
Vol 52 (11) ◽  
pp. 904-911 ◽  
Author(s):  
M. Buti ◽  
T. Giordani ◽  
M. Vukich ◽  
L. Gentzbittel ◽  
L. Pistelli ◽  
...  
Keyword(s):  
Helianthus Annuus ◽  
Sequence Similarity ◽  
Protein Domain ◽  
Long Terminal Repeats ◽  
High Sequence Identity ◽  
Nonsense Mutations ◽  
Reading Frame ◽  
Sequence Identity ◽  
Isolation And Characterization ◽  
Copia Retrotransposon

In this paper we report on the isolation and characterization, for the first time, of a complete 6511 bp retrotransposon of sunflower. Considering its protein domain order and sequence similarity to other copia elements of dicotyledons, this retrotransposon was assigned to the copia retrotransposon superfamily and named HACRE1 ( Helianthus annuus copia-like retroelement 1). HACRE1 carries 5′ and 3′ long terminal repeats (LTRs) flanking an internal region of 4661 bp. The LTRs are identical in their sequence except for two deletions of 7 and 5 nucleotides in the 5′ LTR. Based on the sequence identity of the LTRs, HACRE1 was estimated to have inserted within the last ∼84 000 years. The isolated sequence contains a complete open reading frame with only one complete reading frame. The absence of nonsense mutations agrees with the very high sequence identity between LTRs, confirming that HACRE1 insertion is recent. The haploid genome of sunflower (inbred line HCM) contains about 160 copies of HACRE1. This retrotransposon is expressed in leaflets from 7-day-old plantlets under different light conditions, probably in relation to the occurrence of many putative light-related regulatory cis-elements in the LTRs. However, sequenced cDNAs show less variability than HACRE1 genomic sequences, indicating that only a subset of this family is expressed under these conditions.

Sequence Similarity Searching Using the BLAST Family of Programs

1999 ◽  
Vol 46 (1) ◽  
pp. 19.3.1-19.3.29 ◽  
Author(s):  
Tyra G. Wolfsberg ◽  
Thomas L. Madden
Keyword(s):  
Sequence Similarity ◽  
Similarity Searching

scholarly journals SECOM: A Novel Hash Seed and Community Detection Based-Approach for Genome-Scale Protein Domain Identification

PLoS ONE ◽  
2012 ◽  
Vol 7 (6) ◽  
pp. e39475 ◽  
Author(s):  
Ming Fan ◽  
Ka-Chun Wong ◽  
Taewoo Ryu ◽  
Timothy Ravasi ◽  
Xin Gao
Keyword(s):  
Community Detection ◽  
Protein Domain ◽  
Domain Identification ◽  
Genome Scale
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