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The Intronless Genes Database IGD is a non-redundant collection of richly annotated DNA, CDS, and protein sequences of protein coding intronless genes from human genome. The goal is to provide a comprehensive, standard dataset that represents sequence information for a specified class of human genes (intronless genes). It should be noted, though, that IGD has been built using data from public curated databases. Each IGD record has an Entrez Gene database entry.
IGD biological sequences are derived from GenBank records but differ in that each IGD entry is a synthesis of information, not an archived unit of primary search data. Gene, Protein and CDS sequences are derived from Entrez nucleotide, Entrez protein and CCDS databases respectively.

IGD interface


All pages in IGD design have the same page header. The page header links to home page. The footer of every page contains contact address. Each page contains tow menus (Vertical and Horizontal menus):

* Vertical menu features ten tabs:



**The Home tab always leads back to the home page. The home page contains an introduction to IGD in which the motivation and the goal of the database construction were given.



**The Methodology tab always leads to the Methodology page.



The Methodology page describes the different steps used in IGD construction: data extraction, curation, classification and update.



**The Statistics tab always leads to the statistics page.



In this page, some graphical representations were given showing some statistics analysis done on IGD data:
§ length distribution of IGD intronless genes;
§ intronless genes and diseases;
§ chromosomal distribution of intronless genes in IGD;
§ functional classification of intronless genes in IGD according to GO classification;

**The Search tab always leads to the search page(See details below).



**The BLAST tab leads to the BLAST page. This page provides links to BLAST forms of two BLAST programs that allow DNA/protein sequence comparison against IGD. Choose the link for the BLAST program you want. For example, choose "blastn" to search a Human intronless genes database using a nucleotide query. Descriptions of the search types appear to the right of the links.

The links of the BLAST program of the blast page tab lead to BLAST forms that share a common design. Each form has three sections (examples are from nucleotide BLAST):

1. Enter Query Sequence provides a place to input or upload your query sequence.



2. Choose Search Set is where you select a database and optionally limit your search by a subset of the IGD. The default database "Human Intronless Gene", implicitly limits the search to Human. You can use the "Include only" section to limit the database that you have chosen.
For Example:
To search against Human Intronless Gene that were reviewed in RefSeq database, check: "Intronless genes reviewed by RefSeq database" check box in Include only section.



3. Algorithm parameters section lets you change the parameters of the selected BLAST algorithm.



**The Updates tab always leads to the updates page.



**The Download tab always leads to the downloads page.



The Content of IGD database is available for download in FASTA format.
All intronless gene sequences or just those of a specific chromosome could be downloaded .
Example: You are only interested in downloading human intronless genes on chromosome 11:
1. starting at the IGD Home Page (http://bioinfo-cbs.org/igd/), select Download from the vertical menu to get the download page.
2. In the download page, select 11 from the chromosome pull-down menu.
3. Click on the "Download" button to display all human intronless genes on chromosome 11 in FASTA format.
4. Select the sequences, past and copy them anywhere.

**The Other links tab always leads to the other links page. It contains links to useful biological sites and databases



NCBI: The National Center for Biotechnology Information. The NCBI provides access to biomedical and genomic information.
OMIM: Online Mendelian Inheritance in Man. OMIM is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes.
GO: Gene Ontology project. The GO provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.

**The Help tab always leads to the Help page.



In this page a brief description of IGD interfaces and a search guide are provided.

**The Contacts tab always leads to the contact window.

Once this tab is clicked an Outlook window will be open showing the mail address of IGD administrator.
If Outlook Express program is not installed in your platform, you can copy the email address from the footer of the page web.



* Horizontal menu features seven tabs:



In addition to Home, Search, BLAST, and Help tabs described above, Disclaimer, Administration and FAQ tabs are also available.

**The Disclaimer tab always leads to the Disclaimer page.


**The Administration tab always leads to the Administration page.
This page is reserved for IGD staff. A password is required to access at this page.



**The FAQ tab always leads to the FAQ page.
Frequently Asked Questions are listed questions and answers, all supposed to be frequently asked about IGD.



SEARCH


The search page provides an easy way to query the IGD. In fact, two search strategies are offered: Query search and IG viewer.



Query search strategy:

Query search is based on search term providing several ways of seeking: Here are different types of representative queries:


Types of query Exemples
IGD accession number 34
Entrez Gene database accession number GeneID: 10881
Gene official full name (as it is described in Entrez Gene database) transmembrane protein 133
Gene name(symbol) AD031
Gene aliases (symbol) MGC138255


Example: You are interested in actin-related protein T2 gene.
1. Starting at the IGD Home Page (http://bioinfo-cbs.org/igd/), select Search from the pink menu bar or vertical menu to get the search page.
2. Click on "Search query" links.
3. Type "actin-related protein T2" without quotes in the query box (in upper case or lower case).
4. Select Go.
5. To view gene sequence and graphic representation on the chromosome click on "Details" button.



IG viewer strategy

The IG Viewer strategy provides special browsing capabilities for chromosomes in IGD. It shows a list of intronless genes classified by chromosome.
Example: You are interested in browsing all human intronless genes localised on chromosome 13.
1. Starting at the IGD Home Page (http://bioinfo-cbs.org/igd/), select Search from the pink menu bar or vertical menu to get the search page.
2. Click on "browse by IG viewer" to display the human caryotype.
3. Select chromosome 13.
4. If you are interested in a specific gene click on "Details" button.



Truncating

Truncating search terms is a convenient way to find all the records that contain terms that begin with a given text string. Place an asterisk (*) at the end of a search term to find all records with a term that begins with that text string. For example, the truncated search term "actin*" (without quotes) will retrieve all records in the database that contain the word actin, actin-like 7A, actin-like 7B, actin, beta-like 2, actin-like 9, and actin-related protein T2. Searching actin* in the IGD database.
Phrases that include a space in the word after the asterisk will be retrieved too. For example, if you search "actin-like*", the documents contained "actin-like 7A" term will be retrieved too. Left-handed truncation is not possible.

Limits

Limits allow restriction of a search to a defined subset of the database. Limits can be set to restrict a search to a particular subset of IGD.

Limits available in Search Query strategy for the Intronless Gene Database


Limits available in IG viewer strategy for the Intronless Gene Database


Using Limits

Limits are used to refine search results to retrieve only the most relevant queries. In other words limits remove unneeded or unwanted queries. This section provides examples for using limits to:

Limit a Search to a Particular Database subset using Search Query strategy

Example: You are only interested in human intronless genes started by the word "actin" and that have "reviewed" RefSeq status in RefSeq database:
1. starting at the IGD Home Page (http://bioinfo-cbs.org/igd/), select Search from the pink menu bar or menu to get the search page.
2. Click on "Search query" links.
3. Click on the "Limits" button to get to Limits page.
4. Type "actin*" without quotes in the query box.
5. Check "Reviewed" check box and select Go.

Limit a Search to a Particular Database subset using IG viewer strategy

Example: You are interested in all human intronless genes localised on chromosome 11 that have OMIM entries.
1. starting at the IGD Home Page (http://bioinfo-cbs.org/igd/), select Search from the pink menu bar or menu to get the search page.
2. Click on "browse by IG viewer" to display the human caryotype.
3. Click on the "Limits" button to get to Limits page.
4. In the Limits page, select 11 from the chromosome pull-down menu.
5. Check "OMIM" check box from "Include only" section and select Go.

Using More Than One Limit at a time

The two search strategies in IGD allow you to use more than one limit in your search. Here is one example using multiple limit features in an IGD search.
Example: You are interested in all human intronless genes localised on chromosome 11 that have "Reviewed" and "Validated" RefSeq status in RefSeq database and have OMIM entries.
1. starting at the IGD Home Page (http://bioinfo-cbs.org/igd/), select Search from the pink menu bar or menu to get the search page.
2. Click on "browse by IG viewer" to display human caryotype.
3. Click on the "Limits" button to get to Limits page.
4. In the Limits page, select 11 from the chromosome pull-down menu.
5. Check "Reviewed" check box in “Limits by RefSeq Status” section
6. Check "Validated" check box in “Limits by RefSeq Status” section
7. Check "OMIM" check box in "Include only" section and select Go.

IGD data display


IGD provides two display options: summary and full report.
In each display option, in the title section, a query detail is given indicated the query submitted and the number of item found.
Summary: short reports of gene data: provide description of intronless gene data. When you process a query, the results are displayed in the Summary format as shown in Figure below.



The text of the summary includes the IGD Identifier (IGD accession number), Gene Name symbol (as it is described in IGD), Entrez Gene accession number, Official Full Name (as it is described in Entrez Gene database), Other Aliases of the gene, Organism, Chromosome, RefSeq Status of the gene by Ref Seq database, the Mendelian Inheritance in Man (MIM) number for the gene (hyperlinked to OMIM file of the gene), Gene links (hyperlinked to Entrez Gene file of the gene in Entrez Gene database.

Full report of gene is displaying by clicking on the DETAILS button at the end of the Summary format of the gene.



The full report is divided into three parts:
The top part: consists of summary data (described above).
The middle part: is a graphical presentation that shows gene structure and the location of the gene on the chromosome.
The last part: represents the gene sequence and links to protein and CDS sequences of the gene in FASTA format, simplifying their download for use in many applications. Graphical presentations are downloaded from Entrez Gene database. Gene, Protein and CDS sequences are derived from Entrez nucleotide, Entrez protein and CCDS databases respectively.

To display gene sequence in Fasta format, click on 'View Sequence' button.



To display CDS sequence in Fasta format, click on 'View CDS' button.



To display protein sequence in Fasta format, click on 'View Protein' button.




Updates


IGD updates are provided yearly. A daily update is provided by ENTREZ Gene through the Gene links for each record. Updates include records updated to reflect sequence or annotation changes, including complete re-annotation of a genome.

Suppressed Records

IGD records will be suppressed for several reasons:
• Review by NCBI staff and/or collaborators indicates that a record is no longer supported by Entrez Gene.
• Review by NCBI staff and/or collaborators indicates that the re-annotation of record showed that it is no longer intronless gene.
• Review by NCBI staff and/or collaborators indicates that the record is a pseudogene.
• Review by NCBI staff and/or collaborators indicates that the Gene type of the record is not a protein coding (unknown, misc RNA…).



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