scholarly journals Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

2006 ◽  
Vol 34 (Web Server) ◽  
pp. W143-W146 ◽  
Author(s):  
R. Bhadra ◽  
S. Sandhya ◽  
K. R. Abhinandan ◽  
S. Chakrabarti ◽  
R. Sowdhamini ◽  
...  
Keyword(s):  
Web Server ◽  
Protein Domains ◽  
Homology Search ◽  
Remote Homology ◽  
Search Tool

scholarly journals Secret-AAR: a web server to assess the antigenic density of proteins and homology search against bacterial and parasite secretome proteins

Genomics ◽  
2019 ◽  
Vol 111 (6) ◽  
pp. 1514-1516 ◽  
Author(s):  
Fernanda Cornejo-Granados ◽  
Juan Manuel Hurtado-Ramírez ◽  
Rogelio Hernández-Pando ◽  
Adrián Ochoa-Leyva
Keyword(s):  
Web Server ◽  
Homology Search

scholarly journals NeuroBlast: a 3D spatial homology search tool for gene expression

2007 ◽  
Vol 8 (S2) ◽  
Author(s):  
Lydia Ng ◽  
Chris Lau ◽  
Rob Young ◽  
Sayan Pathak ◽  
Leonard Kuan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Homology Search ◽  
Search Tool

Code Optimization of the Subroutine to Remove Near Identical Matches in the Sequence Database Homology Search Tool PSI-BLAST

2010 ◽  
Vol 17 (6) ◽  
pp. 819-823 ◽  
Author(s):  
Mats Aspnäs ◽  
Kimmo Mattila ◽  
Kristoffer Osowski ◽  
Jan Westerholm
Keyword(s):  
Homology Search ◽  
Code Optimization ◽  
Sequence Database ◽  
Search Tool

SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection

2020 ◽  
Author(s):  
Xiaopeng Jin ◽  
Qing Liao ◽  
Hang Wei ◽  
Jun Zhang ◽  
Bin Liu
Keyword(s):  
Supplementary Information ◽  
Homology Detection ◽  
Remote Homology ◽  
Sequence Search ◽  
Search Tool ◽  
Accurate Position ◽  
Scoring Matrix ◽  
User Friendly ◽  
Structural Classification Of Proteins

Abstract Motivation As one of the most important and widely used mainstream iterative search tool for protein sequence search, an accurate Position-Specific Scoring Matrix (PSSM) is the key of PSI-BLAST. However, PSSMs containing non-homologous information obviously reduce the performance of PSI-BLAST for protein remote homology. Results To further study this problem, we summarize three types of Incorrectly Selected Homology (ISH) errors in PSSMs. A new search tool Supervised-Manner-based Iterative BLAST (SMI-BLAST) is proposed based on PSI-BLAST for solving these errors. SMI-BLAST obviously outperforms PSI-BLAST on the Structural Classification of Proteins-extended (SCOPe) dataset. Compared with PSI-BLAST on the ISH error subsets of SCOPe dataset, SMI-BLAST detects 1.6–2.87 folds more remote homologous sequences, and outperforms PSI-BLAST by 35.66% in terms of ROC1 scores. Furthermore, this framework is applied to JackHMMER, DELTA-BLAST and PSI-BLASTexB, and their performance is further improved. Availability and implementation User-friendly webservers for SMI-BLAST, JackHMMER, DELTA-BLAST and PSI-BLASTexB are established at http://bliulab.net/SMI-BLAST/, by which the users can easily get the results without the need to go through the mathematical details. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Bayesian nonparametrics in protein remote homology search

2016 ◽  
Vol 32 (18) ◽  
pp. 2744-2752 ◽  
Author(s):  
Mindaugas Margelevičius
Keyword(s):  
Bayesian Nonparametrics ◽  
Homology Search ◽  
Remote Homology

scholarly journals A Preliminary Metagenome Analysis Based on a Combination of Protein Domains

Proteomes ◽  
2019 ◽  
Vol 7 (2) ◽  
pp. 19
Author(s):  
Yoji Igarashi ◽  
Daisuke Mori ◽  
Susumu Mitsuyama ◽  
Kazutoshi Yoshitake ◽  
Hiroaki Ono ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Bacterial Species ◽  
Protein Domains ◽  
Correlation Coefficients ◽  
Environmental Data ◽  
Protein Domain ◽  
Homology Search ◽  
Metagenomic Data

Metagenomic data have mainly been addressed by showing the composition of organisms based on a small part of a well-examined genomic sequence, such as ribosomal RNA genes and mitochondrial DNAs. On the contrary, whole metagenomic data obtained by the shotgun sequence method have not often been fully analyzed through a homology search because the genomic data in databases for living organisms on earth are insufficient. In order to complement the results obtained through homology-search-based methods with shotgun metagenomes data, we focused on the composition of protein domains deduced from the sequences of genomes and metagenomes, and we utilized them in characterizing genomes and metagenomes, respectively. First, we compared the relationships based on similarities in the protein domain composition with the relationships based on sequence similarities. We searched for protein domains of 325 bacterial species produced using the Pfam database. Next, the correlation coefficients of protein domain compositions between every pair of bacteria were examined. Every pairwise genetic distance was also calculated from 16S rRNA or DNA gyrase subunit B. We compared the results of these methods and found a moderate correlation between them. Essentially, the same results were obtained when we used partial random 100 bp DNA sequences of the bacterial genomes, which simulated raw sequence data obtained from short-read next-generation sequences. Then, we applied the method for analyzing the actual environmental data obtained by shotgun sequencing. We found that the transition of the microbial phase occurred because the seasonal change in water temperature was shown by the method. These results showed the usability of the method in characterizing metagenomic data based on protein domain compositions.

scholarly journals GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics

PLoS ONE ◽  
2012 ◽  
Vol 7 (5) ◽  
pp. e36060 ◽  
Author(s):  
Shuji Suzuki ◽  
Takashi Ishida ◽  
Ken Kurokawa ◽  
Yutaka Akiyama
Keyword(s):  
Homology Search ◽  
Search Tool

scholarly journals RANKPROP: a web server for protein remote homology detection

2008 ◽  
Vol 25 (1) ◽  
pp. 121-122 ◽  
Author(s):  
I. Melvin ◽  
J. Weston ◽  
C. Leslie ◽  
W. S. Noble
Keyword(s):  
Web Server ◽  
Homology Detection ◽  
Remote Homology ◽  
Remote Homology Detection

scholarly journals A sensitive short read homology search tool for paired-end read sequencing data

2017 ◽  
Vol 18 (S12) ◽  
Author(s):  
Prapaporn Techa-Angkoon ◽  
Yanni Sun ◽  
Jikai Lei
Keyword(s):  
Homology Search ◽  
Sequencing Data ◽  
Short Read ◽  
Search Tool
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