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 in publications

 (6)
PMCID: 5320673
PMID: 28222781
DOI: 10.1186/s12955-017-0613-0

[…] g mattina, m cortese, a parrinello, palermo; v provenzano, l ferrara, r ferranti, partinico (pa); d gioia, m conti, palermo., coordinating center : a nicolucci, mc rossi, g lucisano, r memmo - coresearch - center for outcomes research and clinical epidemiology, pescara, italy, data managers and amd regional coordinators : l fontana, f chiaramonte (lazio); r viola, l cotti (marche); r […]

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

[…] in vivo studies have shown that tr4 can bind to dr elements with 0 to 5 spacer nucleotides , , , , . however, the in vivo tr4 consensus recognition motif in any primary tissue is unknown., we used coresearch, the de novo transcription binding site discovery program, from the genomatix data analysis package as well as dreme to identify overrepresented transcription factor binding site motifs […]

PMCID: 3213110
PMID: 22102868
DOI: 10.1371/journal.pone.0026837

[…] 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 […]

PMCID: 3013027
PMID: 21047794
DOI: 10.1074/jbc.M110.154732

[…] for the sequence motifs enriched among the sequences having hnf4 binding. the 1000 bp sequences around the position with the highest binding p value in each gene group were used. we applied the coresearch tool () to the top 50 sequences from the highest signal rates in the chip-seq data for the determination of the preliminarily motifs. using these generated preliminarily motifs, similar […]

PMCID: 3468743
PMID: 19153767
DOI: 10.1007/s00438-009-0423-0

[…] type 3., all in silico analyses were performed using genomatix software (http://www.genomatix.de). matinspector was used to identify any putative promoter elements listed in the matbase database. coresearch was used to identify any novel putative promoter elements. default search parameters were used in all cases., putative promoter elements in the cachs2 and cachs8 promoters were mutated […]


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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.

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