Bioinformatics1

Bioinformatics1 - Bioinformatics Bi1X2010 PartI...

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Bioinformatics Bi1X‐2010 Part I: Public databases Arbel Tadmor
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Overview Obtaining sequence data from the internet Aligning two sequences Using the biologist’s google: BLAST We’ll use hemoglobin as a case study Related reading: Ch. 6 of Stryer (Biochemistry, 7 th edition)
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First stop: wiki
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Structure of human hemoglobin α subunit (141 aa) β subunit (146 aa) Iron‐ containing heme group In adults hemoglobin is a tetramer: α 2 β 2 Each subunit contains a non‐protein heme group (that holds an iron) The iron binds to an oxygen (shifting absorbance from blue to red) Multiple subunits give rise to cooperatively in oxygen binding and unbinding allowing this protein to release more oxygen in the tissues (making it a good transporter. Further reading Ch. 7 of Stryer
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Let’s focus on the α 1 subunit of hemoglobin. This gene is called HBA1 On which chromosome is this gene?
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Let’s look up this gene Go to the PubMed website: google pubmed ( http://www.ncbi.nlm.nih.gov/PubMed/ ) Search for HBA1 under gene category click
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We’ll start with human hemoglobin click RefSeq accession number XX_# cattle human frog : etc. More about the RefSeq database here… http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch18 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/pdf/gki025.pdf
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Which sequence should we pick? Genomic? mRNA? Protein? Genomic view of HBA1 Genomic context of HBA1 click
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Where HBA1 falls on chromosome 16 our gene chromosome 16 transcriptome
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Genomic context click
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What is the length of … The genomic sequence (NC_...)? The mRNA sequence (NM_…)? The protein sequence (NP_…)? Hint: Double click on gene then Right click→ properties… RefSeq codes: NC_123456 Genomic Mixed Complete genomic molecules including genomes, chromosomes, organelles, plasmids. NM_123456 mRNA Mixed Transcript products; mature messenger RNA (mRNA) transcripts. NP_123456 NP_123456789 Protein Mixed Protein products; primarily full‐length precursor products but may include some partial proteins and mature peptide products. double click
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Genomic vs. mRNA vs. protein sequences NM_000558.3: mRNA-hemoglobin, alpha 1 total range: NC_000016.9 (226,679..227,520) total length: 842 processed length: 576 mRNA product length: 576 mRNA join(226679..226810,226928..227132,227282..227520) /gene="HBA1" /product="hemoglobin, alpha 1" /note="Derived by automated computational analysis using gene prediction method: BestRefseq." /transcript_id="NM_000558.3" /db_xref="GeneID:3039" /db_xref="GI:14456711" HBA1 total range: NC_000016.9 (226,679..227,520) total length: 842 gene 226679..227520 /gene="HBA1" /note="Derived by automated computational analysis using gene prediction method: BestRefseq." /db_xref="GeneID:3039" /db_xref="HGNC:4823"
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