NEIBank: Tips & FAQ
NEIBank Basics
For a detailed description of the NEIBank website and its features, please refer to our July 2008 paper, NEIBank: Genomics and bioinformatics resources for vision research,
published in Molecular Vision: click here to view the paper.
NEIBank is a database of assembled EST data from eye tissue libraries. A summary of all NEIBank libraries can be viewed at the Library Summary Page.
- Click on the eyeball illustration or the text links to see lists of expressed sequence tag analyses of eye tissues. These are assemblies of randomly sequenced cDNA clones.
- Assemblies are displayed in library listing pages.
- Clones that match known sequences from GenBank or match each other are grouped together and identified by RefSeq or GenBank representative sequences, by corresponding Unigene Clusters and Entrez Gene ID.
- The number of clones is shown in the right column. In the default view, expressed genes are listed in order or abundance of their cDNA clones.
- Some clones from the region of particular gene may not always group together. This may be due to relatively poor sequence quality or because the clone comes from an intron or distant flank region of a gene. To get an overview of all the cDNA clones in the region of a particular gene, use EyeBrowse.
- Note that NEIBank libraries have the highest level of curation. Other libraries from dbEST have not received the same level of attention. Some are of very high quality, some are of lesser quality. Very small libraries and those with specific issues of quality or origin of tissue are included in the "Other" category.
- The [**] symbol next to the UniGene identifier indicates that this UniGene appears elsewhere else in the table for a group with a different RefSeq or GenBank match. Click and the second group will show up. There occurs because separate RefSeqs are often assigned to genes with variant transcripts, and sometimes RefSeqs do not cover complete 5' and 3' flanking regions.
Back to Tips & FAQ top
Searching NEIBank Data
NEIBank data can be searched through the Search NEIBank Data Page. More details about how to search NEIBank data is provided below.
- Searching by Library
- Browse the library page listings. Select the tissue or organism from the hypertext on the NEIBank homepage.
- The library page listings display the assembled clones in order of frequency. Data for each library can also be viewed by chromosome location or by keyword. Keywords are extracted from Gene Ontology (GO). High level and lower level (detailed) keywords are available.
- Each group is annotated with GenBank and UniGene descriptions with links to the Entrez, GenBank, UniGene, and chromosome location information. Click on the highlighted number of clones to see a listing of the NEIBank identifiers of the clones in that group or cluster. Follow links to view the sequences or to order clones from our distributors.
- Viewed sequences can be aligned with available genome builds using BLAT. Align at UCSC to see a global view of expressed genes. Align at EyeBrowse to see only eye-expression data, including EyeSAGE. The EyeBrowse view will also show clones that align in this region but did not group with others as described above.
- Note that NEIBank libraries have the highest level of curation. Other libraries from dbEST have not received the same level of attention. Some are of very high quality, some are of lesser quality. Very small libraries and those with specific issues of quality or origin of tissue are included in the "Other" category.
- Searching by Search Term
- Use the Search NEIBank Data page to search for specific clones by NEIBank clone name, by clone GenBank accession number, by Unigene, Entrez Gene ID or GenBank accession number of representative sequences for a specific gene.
- Clones can also be searched by GO terms.
- Select individual libraries (e.g. NEIBank human lacrimal gland unnormalized) or combined NEIBank libraries (for human, mouse or zebrafish).
- The search results displays the matching group or groups with links to the library page listings.
- The group is annotated with GenBank and UniGene descriptions with links to the Entrez, GenBank, UniGene, and chromosome location information. Click on the highlighted number of clones to see a listing of the NEIBank identifiers of the clones in that group or cluster. Follow links to view the sequences or to order clones from our distributors.
- Viewed sequences can be aligned with available genome builds using BLAT. Align at UCSC to see a global view of expressed genes. Align at EyeBrowse to see only eye-expression data, including EyeSAGE. The EyeBrowse view will also show clones that align in this region but did not group with others as described above.
Back to Tips & FAQ top
Disclaimer: Some links from this site may link you to sites outside of NEIBank. NEIBank is not responsible for the content of any non-NEIBank site.
Please send questions/comments on NEIBank scientific content to neibank.comments@nei.nih.gov.
Technical questions/comments regarding the NEIBank website can be sent to neibank.webmaster@nei.nih.gov.
