What does the KEGG database output?Why are metabolic networks important?In model SEED what information can you get regarding gene finding ?1Dr. Balan PhD Tutorial 8
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UNIVERSITY of HOUSTONDepartment of BiotechnologyBTEC 4300/6304* Principles of Bioinformatics/Computational Methods in BiotechnologyantiSMASH fungal versionThis time we are going to be using antiSMASH to search for any biosynthetic gene clusters responsible for polyketide synthases and no ribosomal peptide synthase in a fungal genome. As usual we will be going to NCBI to get the DNA sequence. In this case we will be getting chromosome 1 from candida albicans. Where can I get the whole genome file?What are biosynthetic gene clusters?For antiSMASH how long does it take for it to complete a job?Do you get different results when you submit a FASTA or GenBank file or can we disregard the file type?2Dr. Balan PhD Tutorial 8
UNIVERSITY of HOUSTONDepartment of BiotechnologyBTEC 4300/6304* Principles of Bioinformatics/Computational Methods in BiotechnologyGENSCANFor the example we will be using a section from the human chromosome 8 (GenBank: AF200455.5).What does GENSCAN do ?What parameters are we going to use?On the output what information do we get? What is the exon score contingent on?If we want peptide sequences only, how can we achieved this?explanation: Performing a BLAST search on all predicted protein products1.Copy and paste all predicted protein products into BLAST query box.2.Look through top results of each BLAST result. For this example, look at query sequences less than 100aa.What protein did this AMP (antimicrobial peptide) happen to be?3Dr. Balan PhD Tutorial 8
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