Decrease redundancy statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

Decrease redundancy specifications

Information


Unique identifier OMICS_05168
Name Decrease redundancy
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Elisabeth Gasteiger

Publication for Decrease redundancy

Decrease redundancy citations

 (20)
call_split

Distribution of siderophore gene systems on a Vibrionaceae phylogeny: Database searches, phylogenetic analyses and evolutionary perspectives

2018
PLoS One
PMCID: 5812596
PMID: 29444108
DOI: 10.1371/journal.pone.0191860
call_split See protocol

[…] tabank. The literature search was done over several months during fall 2016. Updated RefSeq accession numbers for identified proteins with the ‘WP’ prefix (the ‘WP’ accession prefix was introduced to decrease redundancy in RefSeq, and has replaced the ‘YP’, ‘NP’ and ‘ZP’ prefixes) are presented in Tables and . These sequences were next used as queries in BLASTp searches to find homologous protein […]

library_books

Cyanobacterial photosynthesis under sulfidic conditions: insights from the isolate Leptolyngbya sp. strain hensonii

2018
PMCID: 5776472
PMID: 29328062
DOI: 10.1038/ismej.2017.193

[…] . Reference datasets were populated by detecting homologs in IMG genomic databases by BLASTP (). Protein sequences were aligned with MUSCLE () and redundancy in the alignments was reduced through the Decrease Redundancy Program (http://web.expasy.org/decrease_redundancy/). Maximum likelihood trees were constructed using PhyML () with the LG+gamma model, 4 gamma rate categories, 10 random starting […]

library_books

Novel arsenic transforming bacteria and the diversity of their arsenic related genes and enzymes arising from arsenic polluted freshwater sediment

2017
Sci Rep
PMCID: 5593903
PMID: 28894204
DOI: 10.1038/s41598-017-11548-8

[…] abase (http://www.ncbi.nlm.nih.gov/), were aligned using MAFFT 7 with iterative refinement by the G-INS-i strategy and then manually refined using Jalview. Redundant sequences were filtered using the Decrease Redundancy tool available at ExPaSy (www.expasy.org) with the following parameters: 99% for maximum similarity and 30% for minimum similarity. Identical sequences were clustered as single OTU […]

library_books

Minimizing proteome redundancy in the UniProt Knowledgebase

2016
PMCID: 5199198
PMID: 28025334
DOI: 10.1093/database/baw139

[…] sed to aid the selection of our Reference proteomes.There are a host of software programs and methods aimed at minimizing redundancy within protein sequence databases. These include SkipRedundant (), Decrease Redundancy (), Pisces (), UniqueProt (), CD-HIT (), FSA-BLAST (), BlastClust (ftp://ftp.ncbi.nih.gov/blast/documents/blastclust.html), MinSet (), BlastCuller (), FastCluster (), Leaf (), UCLU […]

call_split

Genome wide analysis of autophagy associated genes in foxtail millet (Setaria italica L.) and characterization of the function of SiATG8a in conferring tolerance to nitrogen starvation in rice

2016
BMC Genomics
PMCID: 5062844
PMID: 27733118
DOI: 10.1186/s12864-016-3113-4
call_split See protocol

[…] opsis information resource (https://www.arabidopsis.org/). The NtATG, ZmATG, and OsATG protein sequences were downloaded from (www.phytozome.net/) [–]. All redundant sequences were removed using the ‘decrease redundancy’ tool at http://web.expasy.org/decrease_redundancy/. Each putative SiATG gene sequence was checked by SMART (http://smart.embl-heidelberg.de/) to confirm the presence of the ATG do […]

library_books

LRR RLK family from two Citrus species: genome wide identification and evolutionary aspects

2016
BMC Genomics
PMCID: 4982124
PMID: 27515968
DOI: 10.1186/s12864-016-2930-9

[…] th (<100 aa) or large inserted gap regions were removed. Gap-rich columns were further filtered using trimAl v.1.3 with the gappyout method []. To optimize the datasets for evolutionary analyses, the Decrease Redundancy tool, available as a resource at ExPaSy (www.expasy.org), was used to remove identical or distantly related sequences. The Decrease Redundancy parameters were set as 99 for “% max […]

Citations

Looking to check out a full list of citations?

Decrease redundancy institution(s)
Swiss Institute of Bioinformatics, Centre Médical Universitaire, Geneva, Switzerland

Decrease redundancy reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Decrease redundancy