HYPO: A Database of Human Hypothetical Proteins
| Autor: | Anuj Kumar, Partha Sarathi Das, Prashanth Suravajhala, Achuthsankar S. Nair, Shidhi P R, Johny Ijaq, Girik Malik, Vijayaraghava Seshadri Sundararajan, Pawan K. Dhar |
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| Rok vydání: | 2018 |
| Předmět: |
0301 basic medicine
Database Java Application programming interface Computer science Computational Biology Proteins General Medicine computer.software_genre Orphan gene Biochemistry Genome Set (abstract data type) User-Computer Interface 03 medical and health sciences Annotation 030104 developmental biology Structural Biology Humans Human genome UniProt Databases Protein computer computer.programming_language |
| Zdroj: | Protein & Peptide Letters. 25:799-803 |
| ISSN: | 0929-8665 |
| Popis: | Background There are genes whose function remains obscure as they may not have similarities to known regions in the genome. Such known 'unknown' genes constituting the Open Reading Frames (ORF) that remain in the epigenome are termed as orphan genes and the proteins encoded by them but having no experimental evidence of translation are termed as 'Hypothetical Proteins' (HPs). Objectives We have enhanced our former database of Hypothetical Proteins (HP) in human (HypoDB) with added annotation, application programming interfaces and descriptive features. The database hosts 1000+ manually curated records of the known 'unknown' regions in the human genome. The new updated version of HypoDB with functionalities (Blast, Match) is freely accessible at http://www.bioclues.org/hypo2. Methods The total collection of HPs were checked using experimentally validated sets (from Swiss-Prot) or non-experimentally validated set (TrEMBL) or the complete set (UniProtKB). The database was designed with java at the core backend, integrated with databases, viz. EMBL, PIR, HPRD and those including descriptors for structural databases, interaction and association databases. Results The HypoDB constituted Application Programming Interfaces (API) for implicitly searching resources linking them to other databases like NCBI Link-out in addition to multiple search capabilities along with advanced searches using integrated bio-tools, viz. Match and BLAST were incorporated. Conclusion The HypoDB is perhaps the only open-source HP database with a range of tools for common bioinformatics retrievals and serves as a standby reference to researchers who are interested in finding candidate sequences for their potential experimental work. |
| Databáze: | OpenAIRE |
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