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The following problems involve using the Basic Local Alignment Search Tool or BLAST. Using NCBI’s BLAST search page answer the following:

http://blast.ncbi.nlm.nih.gov/Blast.cgi

Remember:

1) Choose the non-redundant or “nr” database to access non-human, non-mouse genome data.

2) E value: a negative value or zero is the best value

3) Some proteins have a putative conserved domain which can be accessed by a protein blast.

Problem 1:

Using this DNA (nucleotide) sequence answer the following questions:

à ATGAAATTCACGATTCAAAAAGATCGTCTTGTTGAAAGTGTCCAAGATGTATTAAAAGCAGTTTCATCCA GAACCACGATTCCCATTCTGACTGGTATTAAAATTGTTGCATCAGATGATGGAGTATCCTTTACAGGGAG TGACTCAGATATTTCTATTGAATCCTTCATTCCAAAAGAAGAAGGAGATAAAGAAATCGTCACTATTGAA CAGCCCGGAAGCATCGTTTTACAGGCTCGCTTTTTTAGTGAAATTGTAAAAAAATTGCCGATGGCAACTG TAGAAATTGAAGTCCAAAATCAGTATTTGACGATTATCCGTTCTGGTAAAGCTGAATTTAATCTAAACGG ACTGGATGCTGATGAATATCCGCACTTGCCGCAGATTGAAGAGCATCATGCGATTCAGATCCCAACTGAT TTGTTAAAAAATCTAATCAGACAAACAGTATTTGCAGTGTCCACCTCAGAAACACGCCCTATCTTGACAG GTGTAAACTGGAAAGTGGAGCAAAGTGAATTATTATGCACTGCAACGGATAGCCACCGTCTTGCATTAAG AAAGGCGAAACTTGATATTCCAGAAGACAGATCTTATAACGTCGTGATTCCGGGAAAAAGTTTAACTGAA CTCAGCAAGATTTTAGATGACAACCAGGAACTTGTAGATATCGTCATCACAGAAACCCAAGTTCTGTTTA AAGCGAAAAACGTCTTGTTCTTCTCACGGCTTCTGGACGGGAATTATCCAGACACAACCAGCCTGATTCC GCAAGACAGCAAAACAGAAATCATTGTGAACACAAAAGAATTCCTTCAGGCCATTGATCGTGCATCTCTT TTAGCTAGAGAGGGACGCAACAACGTTGTAAAACTGTCCGCAAAACCGGCTGAATCCATTGAAATTTCTT CCAATTCGCCAGAAATCGGTAAAGTTGTGGAAGCAATTGTTGCGGATCAAATTGAAGGTGAGGAATTAAA TATCTCTTTTAGTCCAAAATATATGCTGGATGCACTAAAGGTGCTTGAAGGAGCAGAAATACGCGTAAGC TTTACAGGCGCAATGAGACCTTTCTTAATTCGCACGCCGAATGATGAAACGATTGTACAGCTTATCCTTC CTGTCAGAACCTATTAA ß

1.1 Can you tell which end is the 5’ end? Why?

1.2 Perform a nucleotide blast or BLASTn search of the DNA but only use the first eight rows of bases. What was your top hit? Also record the E-value.

1.3 Now perform BLASTn with the entire sequence and compare this result to the

previous search. Explain what happened to the e-value and why?

1.4 Using the complete DNA sequence perform a BLASTx search. What is the best match now? Record the E-value.

1.5 What is the difference in the BLASTn and BLASTx results?

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Related questions

Thank you to whoever can help =)

The following problems involve using the Basic Local Alignment Search Tool or BLAST.

Using NCBI’s BLAST search page answer the following: http://blast.ncbi.nlm.nih.gov/Blast.cgi

Remember: 1) Choose the non-redundant or “nr” database to access non-human, non-mouse genome data.

2) E value: a negative value or zero is the best value

3) Some proteins have a putative conserved domain which can be accessed by a protein blast.

Using this protein (amino acid) sequence answer the following questions:

MMEFTIKRDYFITQLNDTLKAISPRTTLPILTGIKIDAKEHEVILTGSDSEISIEITIPKTVDGEDIVNI SETGSVVLPGRFFVDIIKKLPGKDVKLSTNEQFQTLITSGHSEFNLSGLDPDQYPLLPQVSRDDAIQLSV KVLKNVIAQTNFAVSTSETRPVLTGVNWLIQENELICTATDSHRLAVRKLQLEDVSENKNVIIPGKALAE LNKIMSDNEEDIDIFFASNQVLFKVGNVNFISRLLEGHYPDTTRLFPENYEIKLSIDNGEFYHAIDRASL LAREGGNNVIKLSTGDDVVELSSTSPEIGTVKEEVDANDVEGGSLKISFNSKYMMDALKAIDNDEVEVEF FGTMKPFILKPKGDDSVTQLILPIRTY

2.1 What is generally the starting amino acid of a protein?

2.2 Perform a protein blast or BLASTp search of the protein. What was your top hit? Also record the E-value.

2.3 What are the conserved domains, if any, from BLASTp?

2.4 Perform a TBLASTn search. What is the best match now? And record the E-value.

2.5 What was the difference in the two results (BLASTp to TBLASTn)?

Thank you to whoever can help! =)

The following problems involve using the Basic Local Alignment Search Tool or BLAST. Using NCBI’s BLAST search page answer the following: http://blast.ncbi.nlm.nih.gov/Blast.cgi

Using JGI’s IMG or NCBI, find the following info for these genes.

3.1 Locus tag SAR_RS02120/Accession #: WP_000784258.1

[SAR0427/Accession #: YP_039879]

Protein name:

Gene symbol:

Top match:

Nucleotide sequence:

Protein sequence:

Identify the open reading frame in the following DNA sequence, the protein that this gene encodes for, its function, and the source. GACTATATCCGGCGTATGAAGAAGGTTTCTACGCTTGACCTGTTGTTCGTTGCGATCATGGGTGTTTCGC CGGCCGCTTTTGCCGCCGACCTGATCGACGTGTCCAAACTCCCCAGCAAGGCTGCCCAGGGCGCGCCCGG CCCGGTCACCTTGCAAGCCGCGGTCGGCGCTGGCGGTGCCGACGAACTGAAAGCGATCCGCAGCACGACC CTGCCCAACGGCAAGCAGGTCACCCGCTACGAGCAATTCCACAACGGCGTACGGGTGGTCGGCGAAGCCA TCACCGAAGTCAAGGGTCCCGGCAAGAGCGTGGCGGCGCAGCGCAGCGGCCATTTCGTCGCCAACATCGC TGCCGACCTGCCGGGCAGCACCACCGCGGCGGTATCCGCCGAGCAGGTGCTGGCCCAGGCCAAGAGCCTG AAGGCCCAGGGCCGCAAGACCGAGAATGACAAAGTGGAACTGGTGATCCGCCTGGGCGAGAACAACATCG CCCAACTGGTCTACAACGTCTCCTACCTGATTCCCGGCGAGGGACTGTCGCGGCCGCATTTCGTCATCGA CGCCAAGACCGGCGAAGTGCTCGATCAGTGGGAAGGCCTGGCCCACGCCGAGGCGGGCGGCCCCGGCGGC AACCAGAAGATCGGCAAGTACACCTACGGTAGCGACTACGGTCCGCTGATCGTCAACGACCGCTGCGAGA TGGACGACGGCAACGTCATCACCGTCGACATGAACAGCAGCACCGACGACAGCAAGACCACGCCGTTCCG CTTCGCCTGCCCGACCAACACCTACAAGCAGGTCAACGGCGCCTATTCGCCGCTGAACGACGCGCATTTC TTCGGCGGCGTGGTGTTCAAACTGTACCGGGACTGGTTCGGCACCAGCCCGCTGACCCACAAGCTGTACA TGAAGGTGCACTACGGGCGCAGCGTGGAGAACGCCTACTGGGACGGCACGGCGATGCTCTTCGGCGACGG CGCCACCATGTTCTATCCGCTGGTGTCGCTGGACGTGGCGGCCCACGAGGTCAGCCACGGCTTCACCGAG CAGAACTCCGGGCTGATCTACCGCGGGCAATCAGGCGGAATGAACGAAGCGTTCTCCGACATGGCCGGCG AGGCTGCCGAGTTCTATATGCGCGGCAAGAACGACTTCCTGATCGGCTACGACATCAAGAAGGGCAGCGG TGCGCTGCGCTACATGGACCAGCCCAGCCGCGACGGGCGATCCATCGACAACGCGTCGCAGTACTACAAC GGCATCGACGTGCACCACTCCAGCGGCGTGTACAACCGTGCGTTCTACCTGTTGGCCAATTCGCCGGGCT GGGATACCCGCAAGGCCTTCGAGGTGTTCGTCGACGCCAACCGCTACTACTGGACCGCCACCAGCAACTA CAACAGCGGCGCCTGCGGGGTGATTCGCTCGGCGCAGAACCGCAACTACTCGGCGGCTGACGTCACCCGG GCGTTCAGCACCGTCGGCGTGACCTGCCCGAGCGCGTTGTAA

This question involves using a database. You will use a database for storage and mining of genome sequences. The procedure to identify the gene and the protein that it encodes is as follows: Look carefully at the DNA sequence and identify the start site for transcription. Click on the DNA sequence from the start site of transcription, select all of the sequence, and copy the sequence. Go to the National Center for Biotechnology Information (NCBI) website http://www.ncbi.nlm.nih.gov/. Click on BLAST on the right-hand side under “Popular Resources.” BLAST is a program that will allow you to find the protein sequence for the DNA sequence (gene) you submit. Next click on blastx (translated nucleotide protein). Paste the DNA sequence into the box under “Entry Query Sequence.” Scroll down and click BLAST. The search may take a few seconds; the page will keep updating until the search is completed. You do not need to enter any parameters in the boxes before you click BLAST. When the search is complete, you will have a figure showing the most homologous results or “sequences producing significant alignments”; and, after that, a list of what these proteins are.

Your protein will be the first one on the list. You can click on the accession number or sequence identifier information to bring up more information. You should be able to find the name, function, size (number of amino acids), and source (name of the organism) for the protein.

Your answer should include the: amino acid sequence of the protein size of the protein identity of the proteinx function of the protein (you may need to do additional online research to find this)

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