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NEIBank: NEIBLAST

Use the form below to BLAST your sequences against NEIBank libraries. Choose program to use and database to search:. All libraries on NEIBank. All NEI libraries on NEIBank. All dbEST libraries on NEIBank. Chicken embryo eye unnormalized NEI (NbLib0105: nax). Chicken whole eye unnormalized NEI (NbLib0104: naw). Cow lens unnormalized NEI (NbLib0125: nbm). Dog cornea unnormalized NEI (NbLib0089: nad). Dog eye minus lens unnormalized NEI (NbLib0080: or). Dog lens unnormalized NEI (NbLib0088: nac). Human feta...

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NEIBank: NEIBLAST | neiblast.nei.nih.gov Reviews
<META>
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Use the form below to BLAST your sequences against NEIBank libraries. Choose program to use and database to search:. All libraries on NEIBank. All NEI libraries on NEIBank. All dbEST libraries on NEIBank. Chicken embryo eye unnormalized NEI (NbLib0105: nax). Chicken whole eye unnormalized NEI (NbLib0104: naw). Cow lens unnormalized NEI (NbLib0125: nbm). Dog cornea unnormalized NEI (NbLib0089: nad). Dog eye minus lens unnormalized NEI (NbLib0080: or). Dog lens unnormalized NEI (NbLib0088: nac). Human feta...
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1 neiblast
2 eyebrowse
3 eye disease genes
4 eyesage
5 candidate disease loci
6 library comparison
7 tips and faq
8 program
9 blastn
10 blastp
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NEIBank: NEIBLAST | neiblast.nei.nih.gov Reviews

https://neiblast.nei.nih.gov

Use the form below to BLAST your sequences against NEIBank libraries. Choose program to use and database to search:. All libraries on NEIBank. All NEI libraries on NEIBank. All dbEST libraries on NEIBank. Chicken embryo eye unnormalized NEI (NbLib0105: nax). Chicken whole eye unnormalized NEI (NbLib0104: naw). Cow lens unnormalized NEI (NbLib0125: nbm). Dog cornea unnormalized NEI (NbLib0089: nad). Dog eye minus lens unnormalized NEI (NbLib0080: or). Dog lens unnormalized NEI (NbLib0088: nac). Human feta...

INTERNAL PAGES

neiblast.nei.nih.gov neiblast.nei.nih.gov
1

Databases available for BLAST search

https://neiblast.nei.nih.gov/docs/blast_databases.html

Databases available for BLAST search. All non-redundant GenBank CDS translations PDB SwissProt PIR PRF. All new or revised GenBank CDS translation PDB SwissProt PIR PRF released in the last 30 days. The last major release of the SWISS-PROT protein sequence database (no updates). Yeast (Saccharomyces cerevisiae) protein sequences. E coli genomic CDS translations. Sequences derived from the 3-dimensional structure Brookhaven Protein Data Bank. Kabat's database of sequences of immunological interest. Databa...

2

FASTA format description

https://neiblast.nei.nih.gov/docs/fasta.html

A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (" ") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA. The nucleic acid codes supported are:. For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:. A alanine P proline B aspartat...

3

Low complexity filtering

https://neiblast.nei.nih.gov/docs/filtered.html

Low complexity sequence found by a filter program is substituted using the letter "N" in nucleotide sequence (e.g., "NNNNNNNNNNNNN") and the letter "X" in protein sequences (e.g., "XXXXXXXXX"). Users may turn off filtering by using the "Filter" option on the "Advanced options for the BLAST server" page. Reference for the DUST program:. Tatusov, R. L. And D J. Lipman. Hancock, J. M. And J S. Armstrong. Reference for the SEG program:. Wootton, J. C. Wootton, J. C. Altschul, S. F.

4

Out-of-frame notation

https://neiblast.nei.nih.gov/docs/oof_notation.html

When protein aligned to the nucleotide there are 6 possibilities of match at any point. In OOF alignment - upper sequence is DNAP - 3-frame translated DNA. Lower sequence is protein. At any position next protein base may be aligned to 6 possible bases in DNAP:. TBO - traditional blast output). 0: 3 nucleotides missing - gap (TBO notation "-"). 1: 2 nucleotides missing - "frameshift -2" (TBO notation " "). 2: 1 nucletide missing - "frameshift -1" (TBO notation " "). OOF alignment with DNAP: DTRGGDTPQKSVFS...

5

NCBI BLAST Advanced Options

https://neiblast.nei.nih.gov/docs/full_options.html

Full list of the BLAST Advanced options. BLASTN Program Advanced Options. BLASTP Program Advanced Options. BLASTX Program Advanced Options. TBLASTN Program Advanced Options. Last modified: Mon July 31, 1997.

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LINKS TO THIS WEBSITE

neibank.nei.nih.gov neibank.nei.nih.gov

NEIBank

https://neibank.nei.nih.gov/links.shtml

EyeSite: Links of Interest. University of Kansas Medical Center Department of Anatomy and Cell Biology. National Center for Biotechnology Information. National Ophthalmic Disease Genotyping Network (eyeGENE). Eye Resources on the Internet. Association of Vision Science Librarians. LensNet's Human Lens Genetic Disease Database. Oakland University Eye Research Institute. The University of Wuerzburg Institute of Human Genetics. The University of Texas MD Anderson Cancer Center. Human Eye Disease Genes.

neibank.nei.nih.gov neibank.nei.nih.gov

NEIBank

https://neibank.nei.nih.gov/Publications.shtml

A summary of all current NEIBank libraries can be viewed at the Library Summary Page. Serial analysis of gene expression (SAGE) in normal human trabecular meshwork. Yutao Liu, Drew Munro, David Layfield, Andrew Dellinger, Jeffrey Walter, Katherine Peterson, Catherine Bowes Rickman,. R Rand Allingham, Michael A. Hauser Mol. Vis. 2011; 17:885-893. View Article. Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation. Simpanya MF, Wistow G, Gao J,.

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NEIBank

https://neibank.nei.nih.gov/About.shtml

Welcome to the EyeSite Website, a resource for the ocular genomics community. Currently, the website includes data for several new human eye cDNA libraries. The site will grow over time to include ESTs from other sources and other species. It will also include links to resources on protein structure, proteomics, microarrays and other topics. A complete summary of all current NEIBank libraries can be viewed at the Library Summary Page. Human Eye Disease Genes. Mouse Eye Phenotype Genes.

neibank.nei.nih.gov neibank.nei.nih.gov

NEIBank: EyeSAGE Data on NEIBank

https://neibank.nei.nih.gov/EyeSAGE/index.shtml

SAGE data from the Duke University Eye Center's EyeSAGE. Serial Analysis of Gene Expression (SAGE; http:/ cgap.nci.nih.gov/SAGE. Was used by the Bowes Rickman. Laboratories to study gene expression in the human retina and RPE and normal trabecular meshwork. EyeSAGE is the database tool for exploring these datasets. Displays tag counts for each dataset. View the expression levels for a particular gene. View the expression patterns for candidate disease regions. The Retina/RPE EyeSAGE dataset. Technical qu...

neibank.nei.nih.gov neibank.nei.nih.gov

NEIBank: Candidate Disease Loci

https://neibank.nei.nih.gov/cgi-bin/CDL/cdlStart.cgi

NEIBank: Candidate Disease Loci.

molvis.org molvis.org

Molecular Vision: NEIBank: Genomics and bioinformaticsresources for vision research

http://www.molvis.org/molvis/v14/a160

1327-1337 http:/ www.molvis.org/molvis/v14/a160. Received 07 May 2008 Accepted 10 July 2008 Published 18 July 2008. Articles by the Authors. NEIBank: Genomics and bioinformatics resources for vision research. Jessica N. Ebright,. Michael A. Hauser,. Section on Molecular Structure and Functional Genomics, National Eye Institute, National Institutes of Health, Bethesda, MD;. Department of Ophthalmology, Duke University Medical Center, Durham, NC;. Is a project for ocular genomics that provides data resourc...

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NEIBank

https://neibank.nei.nih.gov/Credits.shtml

The following individuals have played an integral part in the development of the NEIBank data and website:. If you would like to contact anyone listed above, please send a message to neibank.webmaster@nei.nih.gov. And your comments will be forwarded to the appropriate person. Human Eye Disease Genes. Mouse Eye Phenotype Genes. 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.

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NEIBank: Tips & FAQ

https://neibank.nei.nih.gov/tipsFAQ.shtml

NEIBank: Tips and FAQ. How to Search NEIBank Data. Search by Search Term. 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. Note that NEIBank...

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NEIBank: libraries

https://neibank.nei.nih.gov/cgi-bin/libList.cgi?tissue=ciliary

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NEIBank: Eye Disease Genes - Genes That Affect Vision

https://neibank.nei.nih.gov/cgi-bin/eyeDiseaseGenes.cgi

NEIBank: Eye Disease Genes - Genes That Affect Vision. Human Genome Build: February 2009. Last update: December 2, 2011.

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NEIBank: NEIBLAST

Use the form below to BLAST your sequences against NEIBank libraries. Choose program to use and database to search:. All libraries on NEIBank. All NEI libraries on NEIBank. All dbEST libraries on NEIBank. Chicken embryo eye unnormalized NEI (NbLib0105: nax). Chicken whole eye unnormalized NEI (NbLib0104: naw). Cow lens unnormalized NEI (NbLib0125: nbm). Dog cornea unnormalized NEI (NbLib0089: nad). Dog eye minus lens unnormalized NEI (NbLib0080: or). Dog lens unnormalized NEI (NbLib0088: nac). Human feta...

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