page_title: Autophagy database
section_title: Use in bioinformatics
hierarchical_section_title: Autophagy database / Use in bioinformatics
caption_attribution_description: English: One use for autophagy database-Protein list
context_page_description: Autophagy database aim to provide a comprehensive list of autophagy-related genes and proteins, whether they are identified as orthologs or homologs of other, potentially related, proteins. Many kinds of information, including sequences, functions, and 3D structures, can be stored, thus making them accessible in a searchable format. Information available in a single source, using a searchable format, would simplify work for future researchers. These sources would then help to accomplish this aim by providing recently published references on autophagy alongside categories such as user ratings, a list of informative reviews, and results of an original analysis. As autophagy can play a role in a host of human diseases, such as those of the heart, liver, and kidney, further understanding its mechanisms is essential. Simplifying the research process with some database would then provide a scientific boon.
context_section_description: Given that these databases are a large store of biological information, these can be used in bioinformatics applications to simplify information collection and analysis. Bioinformatics looks to pair biological discoveries with big data, to aid in improved scientific discoveries. Each database can be utilized to study an autophagic protein or gene of interest, where these databases are maintained by user submissions. Information for each gene can be used to access Entrez, Ensembl, and PubMed. FASTA sequence is also available for sequence analysis using sites such as BLAST. Specific uses available to Autophagy database and Human autophagy database are shown below.
  Autophagy database has several available functions to search for autophagy-related proteins in different species.
   
  A user may access Autophagy database at http://www.tanpaku.org/autophagy/index.html. The image given, "Options for ADb", showcases the variety of options available for this database. All unhighlighted tabs offer additional information and contact information unrelated to gene search. A user may refer to: 
  the Protein list, highlighted yellow, where the user may select an organism and search for Synonyms, Gene ID, and Protein accession, among other functions. These function offer the user multiple options on how to search for information on genes of interest. The options available on Autophagy database for Protein list can be seen in the example given to the right Protein list given to the right. Selecting various options, such as Synonyms, allows the user to search using specific queries.
  matches of autophagy-related proteins amongst homologs and orthologs under the Homologs tab, highlighted in green. This can be used according to the image to the right, Homologs, where orthologs and homologs can be compared between different organisms and taxa by selecting the required boxes.
  search for specific genes. This may be accomplished using Keyword search, highlighted in blue, and may also be used to match a known gene of interest to a certain species. This helps to determine potential orthologs.
  homologs and orthologs to a gene of interest. Homology search, highlighted in orange, can be used to search a FASTA or unformatted text sequence of a known gene. This may aid in finding connected autophagy-related proteins, or in finding homologs or orthologs. Homologs and orthologs can be compared by the user within or amongst species, given different species and taxa options as seen in the associated figure.
  analyze connections between one gene and autophagy genes available in the database. Original Analyses, highlighted in grey, may be used to find potential autophagy-related gene matches to a known gene. To best utilize these functions, the user should refer to the "Download" tab to download all gene files, so that function of Autophagy database can be fully utilized.
  Human autophagy database has available functions for Look for gene and Clustering. 
   
  When accessing http://autophagy.lu/index.html, these options can be accessed. Interested parties may also Submit new human autophagy proteins to the database. A user may utilize the database according to the following options:
  A user may search for a gene by name in Look for gene category. A gene may be sought for using its gene symbol, Ensembl accession number, chromosome location, or a relevant keyword. Simple instructions for how to access a gene of interest using this method are given in the figure for "Look for gene: HADb". Briefly, the user would access the website, select the highlighted tab, and search for their gene of interest using the available tabs given in the associated image. Specifically, the user would select which option they would like to use in the associated table, and then fill in the information for the desired tab, whether it be Symbol or Synonym, Chromosome, Accession number, or Keyword. Once the tab is selected, information can be entered and searched to determine any linked autophagy-related proteins.
  The user may also refer to Clustering where genes may be viewed in alphabetical orde
caption: One use for autophagy database-Protein list
exif: {}