A multiple alignment of the capsid protein sequences of nepoviruses and comoviruses suggests a common structure

1995 ◽  
Vol 140 (11) ◽  
pp. 2041-2053 ◽  
Author(s):  
O. Le Gall ◽  
T. Candresse ◽  
J. Dunez
Keyword(s):  
Capsid Protein ◽  
Protein Sequences ◽  
Multiple Alignment ◽  
Common Structure

MALAKITE: AN AUTOMATIC TOOL FOR CHARACTERISATION OF STRUCTURE OF RELIABLE BLOCKS IN MULTIPLE ALIGNMENTS OF PROTEIN SEQUENCES

2010 ◽  
Vol 08 (03) ◽  
pp. 503-517 ◽  
Author(s):  
BORIS BURKOV ◽  
BORIS NAGAEV ◽  
SERGEI SPIRIN ◽  
ANDREI ALEXEEVSKI
Keyword(s):  
Protein Sequences ◽  
Structural Data ◽  
Multiple Alignment ◽  
Multiple Alignments ◽  
Simple Consideration ◽  
Automatic Tool ◽  
Alignment Analysis

It makes sense to speak of alignment of protein sequences only within the regions, where the sequences are related to each other. This simple consideration is often disregarded by programs of multiple alignment construction. A package for alignment analysis MAlAKiTE (Multiple Alignment Automatic Kinship Tiling Engine) is introduced. It aims to find the blocks of reliable alignment, which contain related regions only, within the whole alignment and allows for dealing with them. The validity of the detection of reliable blocks' was verified by comparison with structural data.

scholarly journals Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

2011 ◽  
Vol 77 (22) ◽  
pp. 8062-8070 ◽  
Author(s):  
Min-Soo Kim ◽  
Eun-Jin Park ◽  
Seong Woon Roh ◽  
Jin-Woo Bae
Keyword(s):  
Capsid Protein ◽  
Protein Sequences ◽  
Single Stranded Dna ◽  
Dna Viruses ◽  
Content Type ◽  
Double Stranded Dna ◽  
Abundance And Diversity ◽  
Ssdna Viruses ◽  
Virus Abundance ◽  
Large Contigs

ABSTRACTIn this study, we investigated the abundance and diversity of single-stranded DNA (ssDNA) viruses in fecal samples from five healthy individuals through a combination of serial filtration and CsCl gradient ultracentrifugation. Virus abundance ranged from 108to 109per gram of feces, and virus-to-bacterium ratios were much lower (less than 0.1) than those observed in aquatic environments (5 to 10). Viral DNA was extracted and randomly amplified using phi29 polymerase and analyzed through high-throughput 454 pyrosequencing. Among 400,133 sequences, an average of 86.2% viromes were previously uncharacterized in public databases. Among previously known viruses, double-stranded DNA podophages (52 to 74%), siphophages (11 to 30%), myophages (1 to 4%), and ssDNA microphages (3 to 9%) were major constituents of human fecal viromes. A phylogenetic analysis of 24 large contigs of microphages based on conserved capsid protein sequences revealed five distinct newly discovered evolutionary microphage groups that were distantly related to previously known microphages. Moreover, putative capsid protein sequences of five contigs were closely related to prophage-like sequences in the genomes of threeBacteroidesand threePrevotellastrains, suggesting thatBacteroidesandPrevotellaare the sources of infecting microphages in their hosts.

scholarly journals Multiple alignment of protein sequences with repeats and rearrangements

2006 ◽  
Vol 34 (20) ◽  
pp. 5932-5942 ◽  
Author(s):  
Tu Minh Phuong ◽  
Chuong B. Do ◽  
Robert C. Edgar ◽  
Serafim Batzoglou
Keyword(s):  
Protein Sequences ◽  
Multiple Alignment
Sign in / Sign up

Export Citation Format

Share Document