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11 Dec 2019

When using BLAST, should BLAST searches of coding regions be performed with their protein sequences or their nucleotide sequences and why?

Also, can BLAST searches of promoter regions only be performed with their nucleotide sequences?

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Related questions

I just need someone to interpret exactually what I'm suppose todo here. I understand how to compare the sequecnces, however Idon't know exactually how to put them in order. also I can't findout how to find the what chromosome the sequence came from. So farall I gather to do from this is to find which segments overlap, addthe length, tell how big the chromesomeContigs and ShotgunSequencing
In this chapter, we discussed how whole–genome shotgun sequencingmethods can be used to assemble chromosome maps. Recall that in thetechnique of shotgun cloning, chromosomal DNA is first digestedwith different restriction enzymes to create a series ofoverlapping DNA fragments called contiguous sequences, or"contigs." The contigs are then subjected to DNA sequencing, afterwhich bioinformatics–based programs are used to arrange the contigsin their correct order on the basis of short overlapping sequencesof nucleotides.

In this Exploring Genomics exercise, you will carry out asimulation of contig alignment to help you understand theunderlying logic of this approach to creating sequence maps of achromosome. For this purpose, you will return to the NationalCenter for Biotechnology Information BLAST site that was used inother Exploring Genomics exercises and apply a DNA alignmentprogram called bl2seq.

Exercise I: Arranging Contigs to Create a Chromosome Map
1. Access BLAST from the NCBI Web site athttp://www.ncbi.nlm.nih.gov/BLAST/. Locate and select the "Aligntwo sequences using BLAST (bl2seq)" category at the bottom of theBLAST home page. The bl2seq feature allows you to compare two DNAsequences at a time to check for sequence similarityalignments.

2. Below are eight contig sequences taken from an actual humanchromosome sequence deposited in GenBank. For this exercise we haveused short fragments; however, in reality contigs are usuallyseveral thousand base pairs long. To complete this exercise, copyand paste two sequences into the Align feature of BLAST and thenrun an alignment (by clicking on "Align"). (Hint: Access thesesequences from the Companion Web site so that you can copy andpaste the sequences easily.) Repeat these steps with othercombinations of two sequences to determine which sequences overlap,and then use your findings to create a sequence map that placesoverlapping contigs in their proper order. A few tips toconsider:

•Develop a strategy to be sure that you analyze alignments for allpairs of contigs.
•Only consider alignment overlaps that show 100 percent sequencesimilarity.
Sequence A
CTAATTTTTTTTGTATTTTTAATAGAGACGAGGTGTCACCATGTTGGACAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCCCACCTCAGCCTCCCAAAGTGCTGGGAT
TACAAGCATGAGCCACCACTCCCAGGCTTTATTTTCTATTTTTTAATTACAGCCATCCTAGTGAATGTGAAGTAGTATCTCACTGAGGTTTTGATTTGCATTTTTCTATGACA
ATGAACAATGTTTCATGTGCTTGTTGGCTGTTTGTATATCCTTTTTGGAGAAATACCAATTCATGTCCTTTGCCCATTTTTAAAGTGGATTGCATGTCTTTTTGTTGTTTAGT
TGTAAAGATGTGGGTTTTTCTTTTGAGACGGAGTCTCGCTGTCGCCTAGGCTGGAGTGCAGAGGCATGATCTCGGCTGACTGCAATCCCCACCTCCTGGCATCAAGAAGTTCT
CCTGCCTCAGCCTTCCAAGTAGCTGGGTTTACAGATGC

Sequence B
CTTTATCTCAGGACAATGAACCCGCAAGGAGAGGAAGAGCCAGTAATTCTATAGAGACTCGGAGGCGCAGGGGGCACGCTTAGTTAGAGTGGTGGTGGTATTTTCAGTGTTTT
CTGGTTTTATGATAAACACAAGCATCAATGTCTCAAGACTTTCATCTTTATCTTTTTTTTTTTTTTTTTTTTTTTCTTGAGACAGGGTTTCCCTCTGTCACCCAGGCTGGAGT
GCATTGGTGGTGTGATCTTGGCTTTCTGTAACCTCGGGCTTCTGGGCTCAAGCCGTTCTACTACCTCAGCCTCCCAAATAGCTAGAACTACAAGCGTGTGCTGCCACACCTGG
CTAATTTGTTGTATTTTATTTATTCATTTATTTTTGTGAAGACAAGGTCTTGCCATGTTGCCCAGGCTGGTCTCAGACTCCTGGGCTCAAGCAATCCACCCACCTTAGTCTCC
CAAAGTGCTGGGATTACAGGCGTGAGCCACCACACCCA

Sequence C
GGAATTTCACTCTTGTTGCCCAAGTTGGAGTGCAATGGCGCGATCTCAGCTCACTGCAACCTCCGCCTCCCAGGTTCAAACGATTCTCCTGCTTCACTCTCCCCAGTAGCTGG
GATTACAGGCTGCACCACCACACCTGGCTAATTTTTTTTGTATTTTTAATAGAGACGAGGTGTCACCATGTTGGACAGGCTGGTCTCGAACTCCTGACCTCAGGTGATCTGCC
CACCTCAGCCTCCCAAAGTGCTGGGATTACAAGCATGAGCCACCACTCCCAGGC

Sequence D
GCTTCATCTTTCTCTTCACCGTAAAACAGGAAAGTGTGTGGTGACCAGTATTTTAAGGGAAAGGCACTTACAGAGAATTAAGCATTTGACAAAATTTATTTACAGATATTTGT
CTGTGGACCACTTCCGCACCAGCTGTGCATGAGAGGGCTCATTGCTCTGAATTTGCCTCCTTGTCTGCACCCAGGAGACCGTTTCCCAGATCACGCAAACGCTGCCTTCTCCC
CACACCAGGGCCCTCAGCATGGGAATGACCTTCCAGCGCTGCACGTTTCCAATCCATGCTCTGTTTTTCAGTTCTGGCTCACAGAGGACTGCTGGTTGCAAGCAAACTTGTAT
CTGGGTCTTCA

Sequence E
CCTTAAGTGATCTACCTGTCTCTGCCTCTCAAAGTGCTGGGATTGCAGGCATAAGCCGCCATGCCCGGCCCAAAGTTTCTTTATATGTGCTGGATACTAGGCCCGTAACAGAT
ATACAATTTGTAAATATTTTCTCTCATTTTGAAGATTTTCTTTTCACTTTCTTGATAATGTCCTTTGTGTATTTTTTGATAATGTCCTTTGATACACAAAAGTTTTTAAGTTT
GATGAAGTTCAATTTACCTATTATTTTCTTTTGTTGTTCAT

Sequence F
TGTTTGTTTGTTTGTTTTGTTTCATTTTGTTTTTGAGACAGAGTCTTGTTCTGTCGCCCAGTGTAGAGTGCAGTGGCATAATCTCGGCTCACCGTAACCTCCGCCTCCCGGGT
TCAAGCAACTCTGCCTGCCTCAGCCTCCCAAGGAGCTGGGATTATAGACGCCCACCACCATGCCTGGTTAATTTTTGTAGTTTTTTTTAGTAGAGATGGGGTTTTGCCATTTT
GGCCAGGCTGGTCTTGAACTCCTGACCTCAGGTGATCTGCCCACCCTGGCCTCTCAAAGTGCTGGGATTACAGGTGTGAGCTGCCACACTCGGCCACAACAAATTTTTGCACC
AGTTGCTCACA

Sequence G
TCCTTTGATACACAAAAGTTTTTAAGTTTGATGAAGTTCAATTTACCTATTATTTTCTTTTGTTGTTCATTCATTTTGTGTCCTATGTAGGAATCTATTGCCAAATTCAAGGT
GATAAAGATTTACCCCTATGTTTCCTTCTAAGAGTTTTATTGTTTTAGCCCTGATATTTAGCTAAACTTAATTGATTTATTAAGTTTAATTTTCCTATGTGGTATGAAGTCAT
TTATCTTCTTTAGTTCAGGATCCAAGTGAAAGGGGCATCTTCTATCTGGGACATGCCATTCTCATGACAGAGGAAAAAGACAAAAAACTGACACATACAATGACTTTAAAACT
TCACTCA

Sequence H
GGGTTTTTCTTTTGAGACGGAGTCTCGCTGTCGCCTAGGCTGGAGTGCAGAGGCATGATCTCGGCTGACTGCAATCCCCACCTCCTGGCATCAAGAAGTTCTCCTGCCTCAGC
CTTCCAAGTAGCTGGGTTTACAGATGCCCACCACCATGCCTGGCTGGTTTTTGTATTTTTAGTAGACACGGGGTTTTACCATGTTGGCCGGGCTGGTCTGGAACTCCTAACCT
TAAGTGATCTACCTGTCTCTGCCTCTCAAAGTGCTGGGATTGCAGGCATAAGCCGCCATGCCCGGCCCAAAGTTTCTTTATATGTGCTGGATACTAGGCCCGTAACAGATATA
CAATTTGTAAA

3. On the basis of your alignment results, answer the followingquestions, referring to the sequences by their letter codes (Athrough H):

a.What is the correct order of overlapping contigs?
b.What is the length, measured in number of nucleotides, of eachsequence overlap between contigs?
c.What is the total size of the chromosome segment that youassembled?
d.Did you find any contigs that do not overlap with any of theothers? Explain.
4. Run a nucleotide–nucleotide BLAST search (BLASTn) on any of theoverlapping contigs to determine which chromosome these contigswere taken from, and report your answer.
segment is, and what chromosome it came from. here's theassignment. I just need someone to interpret how I should go aboutdoing this.

PLEASE SOMEONE 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.

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?

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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