CoreSearch statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

CoreSearch specifications

Information


Unique identifier OMICS_26749
Name CoreSearch
Interface Web user interface
Restrictions to use License purchase required
Input data Some DNA sequences.
Input format EMBL,FASTA,GCG,RSF,GenBank,IG
Output data All motif matches including: location within the input sequence, sequence of the motif match and similarity to the motif (matrix similarity).
Computer skills Basic
Stability Stable
Free trial Yes
Registration required Yes
Maintained Yes

Maintainers


  • person_outline GGA Team
  • person_outline Thomas Werne

Additional information


CoreSearch is part of GEMS Launcher, which is part of Genomatix Software Suite. http://www.genomatix.de/online_help/help_gems/CoreSearch.html

Publication for CoreSearch

CoreSearch citations

 (3)
library_books

Biased, Non equivalent Gene Proximal and Distal Binding Motifs of Orphan Nuclear Receptor TR4 in Primary Human Erythroid Cells

2014
PLoS Genet
PMCID: 4014424
PMID: 24811540
DOI: 10.1371/journal.pgen.1004339

[…] uld have gene regulatory (in this case, enhancer) activity.We next performed de novo motif analysis to identify other enriched transcription factor binding sites (TFBS) within distant TR4 peaks using CoreSearch and DREME. This analysis did not reveal any single overrepresented TFBS at any stage of erythroid differentiation (data not shown). For example, at day 14, a variety of sites (including MZF […]

call_split

Deep Sequencing of MYC DNA Binding Sites in Burkitt Lymphoma

2011
PLoS One
PMCID: 3213110
PMID: 22102868
DOI: 10.1371/journal.pone.0026837
call_split See protocol

[…] d as −500 to +100 bp around the start sites of the 159,075 annotated transcripts in ElDorado comprising Refseq, GenBank full-length transcripts and Ensembl records) of the MYC motive as discovered by CoreSearch.CoreSearch (Genomatix) with default settings was employed for a de novo calculation of a MYC-binding motive using the 100 highest ranked genomic intervals . CoreSearch starts with a search […]

library_books

Identification of degenerate motifs using position restricted selection and hybrid ranking combination

2006
Nucleic Acids Res
PMCID: 1702486
PMID: 17130169
DOI: 10.1093/nar/gkl658

[…] ertstetter et al. () observed that functional motifs show a preferred pattern of mismatch locations. Position-specific motifs are awarded higher scores of consensus index (Ci) and are thus favored by CoreSearch (). Unlike YMF, CoreSearch does not fix the positions or contents of mutations in an early stage. Consequently, CoreSearch is more sensitive to noise. Motif lengths and degeneracy, as well […]

Citations

Looking to check out a full list of citations?

CoreSearch institution(s)
Institutfur Saugetiergenelik and 'Inslitul fiir Medizinische Informatik und Systemforschung, GSF-Forschungszentrum fiir Umwelt und Gesundheil GmbH, Oberschleiaheim, Germany
CoreSearch funding source(s)
Supported in part by grant 413-4001-01-IV-BE/B 281-28 of the BMBF.

CoreSearch reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review CoreSearch