Bioinformatics,Bi1X‐2010Part,I:,Public,databasesArbel TadmorOverview• Obtaining,sequence,data,from,the,internet• Aligning,two,sequences• Using&the&biologist’s&google:,BLASTWe’ll&use&hemoglobin&as&a&case&studyRelated,reading:,Ch.,6,of,Stryer (Biochemistry,,7thedition),First,stop:,wikiStructure,of,human,hemoglobi nα&subunit(141,aa)β&subunit(146,aa)Iron‐containing,heme group• In&adults&hemoglobin&is&a&tetramer:&α2β2• 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,StryerLet’s&focus&on&the&α1,subunit,of,hemoglobin.,This,gene,is,called,HBA1On,which,chromosome,is,this,gene?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 categoryclickWe’ll&start&with&human&hemoglobi nclickRefSeq accession,number,XX_#cattlehumanfrog:etc.More,about,the,RefSeq database&here…&http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=handbook&part=ch18http://www.ncbi.nlm.nih.gov/pmc/articles/PMC539979/pdf/gki025.pdfWhich,sequence,should,we,pick?,Genomic?,mRNA?,Protein?Genomic,view,of,HBA1Genomic,context,of,HBA1clickWhere,HBA1,falls,on,chromosome,16…our,genechromosome,16transcriptomeGenomic,contextclickWhat&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_12345 6 Genomic Mixed,Complete,genomic,molecules,including,genomes,,chromosomes,,organelles,,plasmids.NM_123456 mRNA Mixed,Transcript,products;,mature,messenger,RNA,(mRNA),transcripts.,NP_123456NP_123456789 Protein Mixed,Protein,products;,primarily,full‐length,precursor,products,but,may,include,some,partial,proteins,and,mature,peptide,products.double-clickGenomic,vs.,mRNA,vs.,protein,sequences,NM_000558.3: mRNA-hemoglobin, alpha 1total range: NC_000016.9 (226,679..227,520)total length: 842 processed length: 576mRNA product length: 576mRNA join(226679..226810,226928..227132,227282..227520)/gene="HBA1"/product="hemoglobin, alpha 1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/transcript_id="NM_000558.3"/db_xref="GeneID:3039"/db_xref="GI:14456711"HBA1total range: NC_000016.9 (226,679..227,520)total length: 842gene 226679..227520/gene="HBA1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/db_xref="GeneID:3039"/db_xref="HGNC:4823"/db_xref="MIM:141800"GenomicmRNANP_000549.1: alpha 1 globintotal range: NC_000016.9 (226,716..227,410)total length: 695processed length: 429 protein product length: 142CDS join(226716..226810,226928..227132,227282..227410)/gene="HBA1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/codon_start=1/product="alpha 1 globin"/protein_id="NP_000549.1"/db_xref="CCDS:CCDS10399.1"/db_xref="GeneID:3039"/db_xref="GI:4504347"proteinGenomic,vs.,mRNA,vs.,protein,sequences,NM_000558.3: mRNA-hemoglobin, alpha 1total range: NC_000016.9 (226,679..227,520)total length: 842 processed length: 576mRNA product length: 576mRNA join(226679..226810,226928..227132,227282..227520)/gene="HBA1"/product="hemoglobin, alpha 1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/transcript_id="NM_000558.3"/db_xref="GeneID:3039"/db_xref="GI:14456711"HBA1total range: NC_000016.9 (226,679..227,520)total length: 842gene 226679..227520/gene="HBA1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/db_xref="GeneID:3039"/db_xref="HGNC:4823"/db_xref="MIM:141800"GenomicmRNANP_000549.1: alpha 1 globintotal range: NC_000016.9 (226,716..227,410)total length: 695processed length: 429 protein product length: 142CDS join(226716..226810,226928..227132,227282..227410)/gene="HBA1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/codon_start=1/product="alpha 1 globin"/protein_id="NP_000549.1"/db_xref="CCDS:CCDS10399.1"/db_xref="GeneID:3039"/db_xref="GI:4504347"proteinQuestion,1Why,is,the,protein,product length,142x3,=,426bp,shorter,than,the,protein,processed length,=,429bp?The,stop,codon was,removedGenomic,vs.,mRNA,vs.,protein,sequences,NM_000558.3: mRNA-hemoglobin, alpha 1total range: NC_000016.9 (226,679..227,520)total length: 842 processed length: 576mRNA product length: 576mRNA join(226679..226810,226928..227132,227282..227520)/gene="HBA1"/product="hemoglobin, alpha 1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/transcript_id="NM_000558.3"/db_xref="GeneID:3039"/db_xref="GI:14456711"HBA1total range: NC_000016.9 (226,679..227,520)total length: 842gene 226679..227520/gene="HBA1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/db_xref="GeneID:3039"/db_xref="HGNC:4823"/db_xref="MIM:141800"GenomicmRNANP_000549.1: alpha 1 globintotal range: NC_000016.9 (226,716..227,410)total length: 695processed length: 429 protein product length: 142CDS join(226716..226810,226928..227132,227282..227410)/gene="HBA1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/codon_start=1/product="alpha 1 globin"/protein_id="NP_000549.1"/db_xref="CCDS:CCDS10399.1"/db_xref="GeneID:3039"/db_xref="GI:4504347"proteinQuestion,1Why,is,the,protein,product length,142x3,=,426bp,shorter,than,the,protein,processed length,=,429bp?The,stop,codon was,removedGenomic,vs.,mRNA,vs.,protein,sequences,NM_000558.3: mRNA-hemoglobin, alpha 1total range: NC_000016.9 (226,679..227,520)total length: 842 processed length: 576mRNA product length: 576mRNA join(226679..226810,226928..227132,227282..227520)/gene="HBA1"/product="hemoglobin, alpha 1"/note="Derived by automated computational analysis usinggene prediction method: BestRefseq."/transcript_id="NM_000558.3"/db_xref="GeneID:3039"/db_xref="GI:14456711"HBA1total range: NC_000016.9 (226,679..227,520)total length: 842gene 226679..227520/gene="HBA1"/note="Derived by automated computational analysis usinggene prediction method: