GENOMICS AND BIOINFORMATICS LAB.

Added on -2019-09-20

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GENOMICS AND BIOINFORMATICS LABName ______________________5 pointsLab __________________________Part 2: BioinformaticsIn this activity you will learn how to use various programs on the internet that allow you to search for and manipulateDNA and protein sequence data. Many of the programs are available through government run websites such as the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI).BLASTA BLAST search is a way to identify protein or DNA sequences related to the one you are interested in. BLAST stands for Basic Local Alignment Search Tool. The emphasis of this tool is to find regions of sequence similarity, which will yield functional and evolutionary clues about the structure and function of your novel sequence. A blast website can be found at: http://blast.ncbi.nlm.nih.gov/Blast.cgiAt this website you will want to use either “nucleotide blast” or “protein blast”.How to “BLAST”: Click “nucleotide blast” or “protein blast” depending on type of sequence. Copy sequence (either DNA or amino acid), and paste it within box on webpage. Under the database pull-down menu, select “nucleotide collection” for nucleotide or “non-redundant protein sequence” for proteins. Next, click on “Blast” at bottom of page. Results will appear in several seconds. Scroll down to see matches. Click on a match to get more details.Restriction Digest AnalysisThere are several programs that search a DNA sequence for known restriction sites – very useful when trying to clone a gene. A nice complete site is: http://tools.neb.com/NEBcutter2/index.phpHow to “digest” a DNA sequence: Copy and paste a nucleotide sequence into the box on the webpage. Click “submit” on the right side. You will then see a map of your sequence with many different restriction sites. You can click on the lower right tab “0 cutters” or “1 cutters” to see which enzymes do not digest the sequence and which ones digest it only once.Nucleotide TranslationTranslating a DNA sequence into an amino acid sequence can be time consuming. Fortunately there are programs available that can do it in a blink of an eye. This website provides a good program for translating DNA sequence:http://www.ebi.ac.uk/Tools/emboss/transeq/How to “translate”: Copy and paste DNA sequence into box on website. Click “Run” at lower right. In a few seconds the amino acid sequence will appear (using the single letter name for amino acids).Sequence AlignmentThese programs allow you to align two or more nucleotide or protein sequences. One easy to use site is: http://www.ebi.ac.uk/Tools/emboss/align/Once here, click on the nucleotide link next to Needle (EMBOSS) if you are aligning nucleotide sequences,or the protein link if you are aligning protein sequence.How to “align” two sequences: All you have to do is copy and paste each sequence into the boxes and hit“Submit”
Unknown A1 atgaagacta tcattgcttt gagccacatt ctatgtctgg ttttcgctca aaaacttcct 61 ggtaatgaca acaacatggc aacgctgtgc cttggacacc atgcagtgcc aaacggaacg 121 atagtgaaaa caatcacgaa tgaccaaatt gaagttacta atgctactga gctggttcag 181 agtttctcta caggtgaaat atgcaacagt cctcatcaga tccttgatgg agaaaactgc 241 acactaatag atgctctatt gggagatcct cagtgtgatg gcttccaaaa caataaatgg 301 gacctttttg ttgaacgaag caaagcccac agcaactgtt acccttatga tgtgtcggat 361 tatgcctccc ttaggtcact agttgcctca tccggtacac tggagtttaa caatgaaagc 421 ttcaattgga ctggagtaac tcaagacgga gcaagctctg cttgcaaaag gagatccagc 481 aaaagtttct ttagtagatt gaattggttg actcacttaa acttcaaata cccagcattg 541 gaagtgacta tgccaaacaa tgaacaattt gacaaattgt acatttgggg ggttcaccac 601 ccggctacgg acaaggacca aatctccctg tatgctcaag cagcaggaag aatcatagta 661 tctaccaaaa gaagccaaca agctgtaatt ccgaatatcg ggtctagacc cagagtaagg 721 gatatcccta gcagaataag catctattgg acaatagtaa gaccgggaga catacttttg 781 attaacagca cagggaatct aattgctcct aggggttact tcaaaatacg aagtgggaaa 841 agctcaataa tgagatcaga tgcacccatt ggcaaatgca attctgcatg catcactcca 901 aatggaagca ttcccaatga caaaccattc caaaatgtaa acaggatcac atacggggcc 961 tgtcccagat atgttaagca aaacactctg aaattggcaa caggaatgag aaatatacca 1021 gagaaacaaa ctagaggcat atttggcgca atagctggtt tcatagaaaa tggttgggag 1081 ggaatggtgg atggttggta cggtttcagg catcaaaatt ctgagggaag gggacaagca 1141 gcagatctca aaagcactca agcagcaatc gatcaaatca atgggaagct gaatagattg 1201 atcggaaaaa ccaacgagaa attccatcag atcgaaaaag aattttcaga agtcgaaggg 1261 agaattcagg accttgagaa atatgttgag gacactaaaa tagatctctg gtcatacaac 1321 gcggagcttc ttgttgccct ggagaaccag cacacaattg atctaactga ctcagaaatg 1381 aacaaattgt ttgaaaaaac aaagaagcaa ctgagggaaa atgctgagga tatgggcaat 1441 ggctgtttca aaatatacca caaatgtgac aatgcctgca taggatcaat cagaaacgga 1501 acttatgacc acgatgtgta cagagatgaa gcattaaaca accgattcca gatcaaggga 1561 gttgagctga agtcagagta caaagattgg attctatgga tttcctttgc catatcatgc 1621 tttttgcttt gtgttgcttt gttggggttc atcatgtggg cctgccaaaa aggcaacatt 1681 aagtgcaaca tttgcatttg aUnknown B1 atgaagacta tcattgcttt gagctacatt ctatgtctgg ttttcgctca aaaacttcct 61 ggtaatgaca acaacatggc aacgctgtgc cttggacacc atgcagtgcc aaacggaacg 121 atagtgaaaa caatcacgaa tgaccaaatt gaagttacta atgctactga gctggttcag 181 agttcctcta caggtgaaat atgcaacagt cctcatcaga tccttgatgg agaaaactgc 241 acactaatag atgctctatt gggagatcct cagtgtgatg gcttccaaaa caagaagtgg 301 gacctttttg ttgaacgaag caaagcccat agcaactgtt acccttatga tgtgccggat 361 tatgcctccc ttaggtcact agttgcctca tccggtacac tggagtttaa caatgaaagc 421 ttcaattgga ctggagtaac tcaaaacgga gcaagctctg cttgcaaaag gagatccaac 481 aaaagtttct ttagtagatt gaattggttg actcacttaa acttcaaata cccagcattg 541 gaagtgacta tgccaaacaa tgaacaattt gacaaattgt acatttgggg ggttcaccac 601 ccggctacgg acaaggacca aatctccctg tatgctcaag cagcaggaag aatcatagta 661 tctaccaaaa gaagccaaca agctgtaatt ccgaatatcg ggtctagacc cagagtaagg 721 gatatcccta gcagagtaag catctattgg acaatagtaa gaccgggaga catacttttg 781 attaacagca cagggaatct aattgctcct aggggttact tcaaaatacg aagtgggaaa 841 agctcaataa tgagatcaga tgcacccatt ggcaaatgca attctgcatg catcactcca 901 aatggaagca ttcccagtga caaaccattc caaaatgtaa acaggatcac atacggggcc 961 tgtcccagat atgttaagca aaacactctg aaattggcaa caggaatgag aaatatacca 1021 gagaaacaaa ctagaggcat atttggcgca atagctggtt tcatagaaaa tggttgggag 1081 ggaatggtgg atggttggta cggtttcagg catcaaaatt ctgagggaag gggacaagca

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