miPepBase: A Database of Experimentally Verified Peptides Involved in Molecular Mimicry

Garg, Anjali; Kumari, Bandana; Kumar, Ravindra; Kumar, Manish

This is not a direct way to search the data content of miPepBase. Rather it searches similar sequences and peptides in the miPepBase. The BLAST search option is available at menu bar ( Figure 3E ). The query sequence in FASTA format can either be pasted in the text box or uploaded as sequence file (Step e1). Three parameters have to be optimized for efficient BLAST search (i) the database in which related sequence will be searched; (ii) E-value, and (iii) Scoring Matrix. The default e-value and scoring matrix are 100 and BLOSUM 62, respectively (Step e2). As shown in section E, when P10809 protein sequence was searched against host protein database, total 13 hits were obtained which are arranged on the basis of ascending e-value (Step e3). Also every BLAST hit protein entry is further linked (in blue color) to detailed information page, which provide tabulated detailed information of corresponding BLAST hit (Step e4). These information are the same as described above for keyword search option (Step a4-a6).