PMC:5056897 / 9438-11084
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/5056897","sourcedb":"PMC","sourceid":"5056897","source_url":"https://www.ncbi.nlm.nih.gov/pmc/5056897","text":"Homology and function prediction\nThe assertion of homology between proteins derived on the basis of sequence similarity provides insights into the functional properties of an unknown protein showing similarity with a protein of known function. BLAST [34, 35, 36, 37] is a commonly used and most reliable tool for the purpose. Structure and function prediction help to identify novel drug targets which can be further utilized for therapeutic intervention [38, 39, 40, 41, 42, 43, 44, 45, 46]. We used blastp module to search for homologous proteins to the HPs against a database of nonredundant protein sequences. To decrease the redundancy in the results, a threshold was set for the e-value less than 0.0005 and sequence identity more than 30%. SMART [47] was used for the function prediction. It uses information about domain architecture from known proteins and provides functional annotation of query sequences. Function prediction based on motif discovery was performed using InterProScan [48] and Motif. InterProScan searches the query sequence against Interpro consortium to bring about the function of the proteins using motif information. Motif operates as an interface between user and motif library of known databases. It searches the query sequence against Pfam, TIGRFAM, COG, SMART, PROSITE Patterns, and PROSITE profiles. The user has the facility to choose any of these databases. We also used STRING [49] to predict protein-protein interaction networks for the HPs. It gives functional insights for the HPs based on protein-protein interaction. Information for homology and function prediction is listed in Supplementary Table 4.","divisions":[{"label":"Title","span":{"begin":0,"end":32}}],"tracks":[{"project":"2_test","denotations":[{"id":"27729842-2231712-44840769","span":{"begin":251,"end":253},"obj":"2231712"},{"id":"27729842-26415878-44840770","span":{"begin":255,"end":257},"obj":"26415878"},{"id":"27729842-23615770-44840771","span":{"begin":263,"end":265},"obj":"23615770"},{"id":"27729842-25287765-44840772","span":{"begin":456,"end":458},"obj":"25287765"},{"id":"27729842-26381417-44840773","span":{"begin":460,"end":462},"obj":"26381417"},{"id":"27729842-18930737-44840774","span":{"begin":464,"end":466},"obj":"18930737"},{"id":"27729842-17718721-44840775","span":{"begin":468,"end":470},"obj":"17718721"},{"id":"27729842-17890654-44840776","span":{"begin":472,"end":474},"obj":"17890654"},{"id":"27729842-24260279-44840777","span":{"begin":476,"end":478},"obj":"24260279"},{"id":"27729842-25929263-44840778","span":{"begin":480,"end":482},"obj":"25929263"},{"id":"27729842-26519933-44840779","span":{"begin":488,"end":490},"obj":"26519933"},{"id":"27729842-22053084-44840780","span":{"begin":754,"end":756},"obj":"22053084"},{"id":"27729842-24451626-44840781","span":{"begin":996,"end":998},"obj":"24451626"},{"id":"27729842-23203871-44840782","span":{"begin":1418,"end":1420},"obj":"23203871"}],"attributes":[{"subj":"27729842-2231712-44840769","pred":"source","obj":"2_test"},{"subj":"27729842-26415878-44840770","pred":"source","obj":"2_test"},{"subj":"27729842-23615770-44840771","pred":"source","obj":"2_test"},{"subj":"27729842-25287765-44840772","pred":"source","obj":"2_test"},{"subj":"27729842-26381417-44840773","pred":"source","obj":"2_test"},{"subj":"27729842-18930737-44840774","pred":"source","obj":"2_test"},{"subj":"27729842-17718721-44840775","pred":"source","obj":"2_test"},{"subj":"27729842-17890654-44840776","pred":"source","obj":"2_test"},{"subj":"27729842-24260279-44840777","pred":"source","obj":"2_test"},{"subj":"27729842-25929263-44840778","pred":"source","obj":"2_test"},{"subj":"27729842-26519933-44840779","pred":"source","obj":"2_test"},{"subj":"27729842-22053084-44840780","pred":"source","obj":"2_test"},{"subj":"27729842-24451626-44840781","pred":"source","obj":"2_test"},{"subj":"27729842-23203871-44840782","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#ecd893","default":true}]}]}}