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Blocks Database specifications

Information


Unique identifier OMICS_22512
Name Blocks Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 14.3
Maintained No

Maintainers


This tool is not available anymore.

Additional information


http://blocks.fhcrc.org/blocks/help/tutorial/tutorial.html http://blocks.fhcrc.org/help/bm/help.html#INTRO

Publication for Blocks Database

Blocks Database citations

 (4)
library_books

Metal Dealing at the Origin of the Chordata Phylum: The Metallothionein System and Metal Overload Response in Amphioxus

2012
PLoS One
PMCID: 3419175
PMID: 22905252
DOI: 10.1371/journal.pone.0043299

[…] bioinformatic facilities of the EBI-SRS platform , the main objective being the identification of metal binding functional motifs by using the PROSITE algorithm . Furthermore, a scan was made of the BLOCKS database to identify the most highly conserved regions of protein families contained in the identified sequences . Finally, the Metal Detector (v1.0) software (http://metaldetector.dsi.unifi.it […]

library_books

Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations

2009
BMC Bioinformatics
PMCID: 2745591
PMID: 19758473
DOI: 10.1186/1471-2105-10-S8-S9

[…] tween -0.12 on our data set over 0.25 on human mutagenesis data, up to 0.59 on the HIV-1 protease mutagenesis set in the original SIFT paper []. Although the methodology and underlying data (i.e. the BLOCKS database) is certainly sound, and there is no question that SIFT in most cases can be trusted to evaluate whether or not an amino acid change is tolerated in an evolutionary sense, this variabi […]

library_books

Characterization and comparative sequence analysis of the DNA mismatch repair MSH2 and MSH7 genes from tomato

2009
PMCID: 2770637
PMID: 19690966
DOI: 10.1007/s10709-009-9398-3

[…] NTHER, Pfam, PIRSF, PRINTS, Prodom, PROSITE patterns and profiles, SMART, TIGRFAMS, GENE3D and SUPERFAMILY. In addition, the MOTIF metasite (http://motif.genome.jp/) was also used, which included the BLOCKS database.Predictions of protein structures based on homology modeling were performed using the SAM-T06 program (http://compbio.soe.ucsc.edu/SAM_T06/T06-query.html). This program finds and align […]

library_books

One Block CYRCA: an automated procedure for identifying multiple block alignments from single block queries

2005
Nucleic Acids Res
PMCID: 1160248
PMID: 15980470
DOI: 10.1093/nar/gki488

[…] on block-to-block alignments found by LAMA and CYRCA. This required careful manual intervention since the nuclease-associated modular DNA-binding domains (NUMODs) blocks we found were not part of the Blocks database. Submitting the NUMOD motifs to the One-Block CYRCA server returned the block sets we used to identify their function (). […]

Citations

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Blocks Database institution(s)
Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
Blocks Database funding source(s)
Supported by a grant from the NIH (GM29009).

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