Bioinformatics - Notes PDF

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Bioinformatics  Molecular biology + Computer science  Technology that helps organize, analyze, and store sequence data What did you sequence?  Gene o Introns o Exons o Regulatory regions  Noncoding DNA  What chromosome is the sequence on Public Databases  National Center for Biotechnology Information (NCBI) o Publications (PubMed) o Genes and disease (OMIM o Sequence homology (Homologene) o GenBank (Sequence Repository)  Currently has 200 million sequences o Basic Local Alignment Search Tool (BLAST)  We will use BLAST to compare our sequences to GenBank BLAST searches can give lots of info  Enter your sequence and see what it is  If it is a gene, it can be annotated o What RNA does it encode, What protein does it encode, What is its function, How, when, where is it expressed, Is it found in other species, How similar is in the gene in other species (Homologous, Comparative genomics) Editing your sequence  Trim untrusted regions on the ends of the sequence  Correct N’s in remaining sequence  Delete pUC sequence(s)  May be on only one end of your sequence or both ends, depending on the size of the insert o A larger insert will only have vector on one end and a smaller insert will have vector on both ends Sequence Analysis: Sequence Identity  For your clone sequence and 5 provided sequences, you will o Run a BLAST search to compare your sequences to GenBank  Nucleotide search compares your sequence to other nucleotide sequences

Blastx search will translate your nucleotide sequence into amino acids (in all reading frames) and compare to a database of protein sequences o To do so, simply copy and paste the sequence into the webpage and hit BLAST 

BLAST results include  Graphic summary  Descriptions  Alignments Things to notice  What is the best match?  What is the most likely human chromosome this sequence exists on?  Does your sequence appear to contain any part of a gene sequence? Sequence Analysis: Comparative Genomics  For your clone sequence and 5 provided sequences, you will o Run a BLAT search to compare your sequences to the genome of other organisms  To do so, simply copy and paste the sequence into the webpage, choose the appropriate genome to BLAT from the dropdown menu and hit submit  Only top hit is good one o High score (anything in the 20s or less is not significant) o Good portion of sequence BLATed matches Can you tell the exon-intron structure from looking at the human BLAT results?  No, because both introns and exons match  Must look at more deep relationships, where intron sequence has had time to diverge/change...