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InBase specifications

Information


Unique identifier OMICS_15451
Name InBase
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publications for InBase

InBase citations

 (11)
library_books

Intein Clustering Suggests Functional Importance in Different Domains of Life

2015
Mol Biol Evol
PMCID: 4760082
PMID: 26609079
DOI: 10.1093/molbev/msv271

[…] CBI. Additionally, protein domains and motifs were identified using InterPro protein analysis tool. Other resources heavily used in the present study are: InBase—intein database (http://tools.neb.com/inbase/; Perler ); European Nucleotide Archive (ENA: http://www.ebi.ac.uk/ena/); Genome at NCBI (http://www.ncbi.nlm.nih.gov/genome/); Basic Local Alignment Search Tool (BLAST) programs (http://blast. […]

library_books

Inteins as indicators of gene flow in the halobacteria

2014
Front Microbiol
PMCID: 4071816
PMID: 25018750
DOI: 10.3389/fmicb.2014.00299

[…] Position specific scoring matrices (PSSMs) were created using the collection of all inteins from InBase, the Intein database and registry (Perler, ). A custom database was created with all inteins, and each intein was used as a seed to create a PSSM using the custom database. These PSSMs were the […]

call_split

The haloarchaeal MCM proteins: bioinformatic analysis and targeted mutagenesis of the β7 β8 and β9 β10 hairpin loops and conserved zinc binding domain cysteines

2014
Front Microbiol
PMCID: 3972481
PMID: 24723920
DOI: 10.3389/fmicb.2014.00123
call_split See protocol

[…] rge sequence insertions in comparative sequence analysis. Inteins boundaries were defined by the presence of the N-terminal (block A) and C-terminal (block G) intein splicing motifs as defined at the InBase intein database (Perler, ). […]

library_books

Gene invasion in distant eukaryotic lineages: discovery of mutually exclusive genetic elements reveals marine biodiversity

2013
PMCID: 3749507
PMID: 23635865
DOI: 10.1038/ismej.2013.70

[…] entifiers: Ascomycota, Hca-PRP8; Basidiomycota, Cla-PRP8; Chytridiomycota, Bde-JEL423-PRP8; Mucoromycotina, Pbl-PRP8-a) as queries. Intein splicing motifs flanking the HE domain were identified using InBase data () and aligned using MUSCLE v3.8 () with manual editing. […]

library_books

Quantifying Homologous Replacement of Loci between Haloarchaeal Species

2012
Genome Biol Evol
PMCID: 3542582
PMID: 23160063
DOI: 10.1093/gbe/evs098

[…] lies according to sequence homology, intein sequences were identified and removed from protein coding sequences because they are not present in all homologous ORFs (). Each known intein sequence from InBase () was used as a seed to build position-specific scoring matrices with Position-Specific Initiated Basic Local Alignment Search Tool (BLAST) 2.2.23+ () against InBase and the haloarchaeal prote […]

call_split

The Arthrobacter Species FB24 Arth_1007 (DnaB) Intein Is a Pseudogene

2011
PLoS One
PMCID: 3196547
PMID: 22028863
DOI: 10.1371/journal.pone.0026361
call_split See protocol

[…] Bayesian inference analysis was performed using the Geneious Pro 5.1 suite of programs (Geneious, Auckland, NZ). Briefly, intein splicing domain Motifs A, B, F and G present in the InBase database (http://www.neb.com/neb/inteins.html) were concatenated to produce a single 49 aa sequence for each intein using names defined in InBase, as previously described , . Due to the variabl […]

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InBase institution(s)
New England Biolabs, Inc., Beverly, MA, USA

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