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ChromDB: the chromatin database.

Gendler K, Paulsen T, Napoli C - Nucleic Acids Res. (2007)

Bottom Line: Model animal and fungal proteins are included in the database to facilitate a complete, comparative analysis of the chromatin proteome and to make the database applicable to all chromatin researchers and educators.Chromatin biology and chromatin remodeling are complex processes involving a multitude of proteins that regulate the dynamic changes in chromatin structure which either repress or activate transcription.We strive to organize ChromDB data in a straightforward and comparative manner to help users understand the complement of proteins involved in packaging DNA into chromatin.

View Article: PubMed Central - PubMed

Affiliation: BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA.

ABSTRACT
The ChromDB website (http://www.chromdb.org) displays chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms. Our primary focus is to display sets of highly curated plant genes predicted to encode proteins associated with chromatin remodeling. Our intent is to make this intensively curated sequence information available to the research and teaching communities in support of comparative analyses toward understanding the chromatin proteome in plants, especially in important crop species such as corn and rice. Model animal and fungal proteins are included in the database to facilitate a complete, comparative analysis of the chromatin proteome and to make the database applicable to all chromatin researchers and educators. Chromatin biology and chromatin remodeling are complex processes involving a multitude of proteins that regulate the dynamic changes in chromatin structure which either repress or activate transcription. We strive to organize ChromDB data in a straightforward and comparative manner to help users understand the complement of proteins involved in packaging DNA into chromatin.

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Related in: MedlinePlus

A screen shot of a gene record page along with the side tool bar for accessing database searching, tools, reports and viewers.
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Figure 1: A screen shot of a gene record page along with the side tool bar for accessing database searching, tools, reports and viewers.

Mentions: ChromDB sequences fall into two categories: genomic-based and transcript-based. Genomic-based sequences are limited to plant genomes [A. thaliana, Oryza sativa (japonica cultivar- and indica cultivar-groups), Medicago truncatula, Populus trichocarpa, Physcomitrella patens (moss) and Z. mays] and algal and diatom genomes (Chlamydomonas reinhardtii, Ostreococcus lucimarinus and Phaeodactylum tricornutum). The plant genomes are highlighted on the side toolbar on the ChromDB homepage (shown on the left side in Figure 1). Other important plant species are included in the database as transcript-based sequences which are derived from EST contigs or singlets. The use of EST contigs results in partial sequences especially for larger proteins. For example, ∼200 transcript-based sequences are included in the database for Hordeum vulgare (barley) but only 36% of these transcripts represent the entire, predicted coding sequence. Partial protein sequences, usually protein domains or the C-termini, are used as BLAST queries when identifying EST contigs. The use of a limited span of protein, rather than the entire sequence, limits redundancy that could result from the inclusion of multiple, non-overlapping contigs representing different regions of the same transcript. Transcript-based plant sequences are converted to genome-based as sequencing projects produce sufficient data to make a conversion worthwhile. For example, maize is being converted from transcript-based to genomic-based due to the rapid accumulation of sequence data from large-scale maize genome sequencing projects.Figure 1.


ChromDB: the chromatin database.

Gendler K, Paulsen T, Napoli C - Nucleic Acids Res. (2007)

A screen shot of a gene record page along with the side tool bar for accessing database searching, tools, reports and viewers.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238968&req=5

Figure 1: A screen shot of a gene record page along with the side tool bar for accessing database searching, tools, reports and viewers.
Mentions: ChromDB sequences fall into two categories: genomic-based and transcript-based. Genomic-based sequences are limited to plant genomes [A. thaliana, Oryza sativa (japonica cultivar- and indica cultivar-groups), Medicago truncatula, Populus trichocarpa, Physcomitrella patens (moss) and Z. mays] and algal and diatom genomes (Chlamydomonas reinhardtii, Ostreococcus lucimarinus and Phaeodactylum tricornutum). The plant genomes are highlighted on the side toolbar on the ChromDB homepage (shown on the left side in Figure 1). Other important plant species are included in the database as transcript-based sequences which are derived from EST contigs or singlets. The use of EST contigs results in partial sequences especially for larger proteins. For example, ∼200 transcript-based sequences are included in the database for Hordeum vulgare (barley) but only 36% of these transcripts represent the entire, predicted coding sequence. Partial protein sequences, usually protein domains or the C-termini, are used as BLAST queries when identifying EST contigs. The use of a limited span of protein, rather than the entire sequence, limits redundancy that could result from the inclusion of multiple, non-overlapping contigs representing different regions of the same transcript. Transcript-based plant sequences are converted to genome-based as sequencing projects produce sufficient data to make a conversion worthwhile. For example, maize is being converted from transcript-based to genomic-based due to the rapid accumulation of sequence data from large-scale maize genome sequencing projects.Figure 1.

Bottom Line: Model animal and fungal proteins are included in the database to facilitate a complete, comparative analysis of the chromatin proteome and to make the database applicable to all chromatin researchers and educators.Chromatin biology and chromatin remodeling are complex processes involving a multitude of proteins that regulate the dynamic changes in chromatin structure which either repress or activate transcription.We strive to organize ChromDB data in a straightforward and comparative manner to help users understand the complement of proteins involved in packaging DNA into chromatin.

View Article: PubMed Central - PubMed

Affiliation: BIO5 Institute, University of Arizona, Tucson, AZ 85719, USA.

ABSTRACT
The ChromDB website (http://www.chromdb.org) displays chromatin-associated proteins, including RNAi-associated proteins, for a broad range of organisms. Our primary focus is to display sets of highly curated plant genes predicted to encode proteins associated with chromatin remodeling. Our intent is to make this intensively curated sequence information available to the research and teaching communities in support of comparative analyses toward understanding the chromatin proteome in plants, especially in important crop species such as corn and rice. Model animal and fungal proteins are included in the database to facilitate a complete, comparative analysis of the chromatin proteome and to make the database applicable to all chromatin researchers and educators. Chromatin biology and chromatin remodeling are complex processes involving a multitude of proteins that regulate the dynamic changes in chromatin structure which either repress or activate transcription. We strive to organize ChromDB data in a straightforward and comparative manner to help users understand the complement of proteins involved in packaging DNA into chromatin.

Show MeSH
Related in: MedlinePlus