1. What is the difference between an iterated blast (psi-blast) search and a simple blast search? 2. Arslan sequenced a gene in lab how he will know about the gene either it is novel discovery or gene is already present in the database? 3. Ruwaifa want to compares a nucleotide query sequence what option he will opt in BLAST and why? 4. Uzair has two protein sequences, he want to check their similarities what he will do? What results are expected

1. What is the difference between an iterated blast (psi-blast) search and a simple blast search? 2. Arslan sequenced a gene in lab how he will know about the gene either it is novel discovery or gene is already present in the database? 3. Ruwaifa want to compares a nucleotide query sequence what option he will opt in BLAST and why? 4. Uzair has two protein sequences, he want to check their similarities what he will do? What results are expected

Human Heredity: Principles and Issues (MindTap Course List)

11th Edition

ISBN:9781305251052

Author:Michael Cummings

Publisher:Michael Cummings

Chapter13: An Introduction To Genetic Technology

Section: Chapter Questions

Problem 19QP

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1、You have a 250 bp DNA sequence from a human protein-coding gene. What's the best tool to find out which gene matches this sequence? BLAST A Clustal algorithm (such as Clustal Omega) A Burrows-Wheeler algorithm (such as BWA) Just Google it 2、Sequence alignment algorithms like Burrows-Wheeler were primarily designed to handle many (millions) of short sequences and match them to a reference genome efficiently. Another property of these algorithms makes them suitable for use with RNAseq data. What property is this? Burrows-Wheeler can distinguish which strand of reference genome matches a sequencing read. Burrows-Wheeler can align a sequencing read that matches two different exons. Burrows-Wheeler uses a pre-compiled and compressed index of the reference genome. Burrows-Wheeler can be parallelized.
Devonte sequenced a novel gene using the Sanger dideoxy sequencing method. The resulting sequence he determined is shown below. CCGGATCGGGTTTCCGGGAATCGGGGG Devonte asked his colleague George to verify his results by repeating the sequencing experiment in a different lab. George was disappointed to find that his gel showed just one DNA band with a fluorescently labeled “G.” What did he leave out of the sequencing mixture? Devonte sequenced a novel gene using the Sanger dideoxy sequencing method. The resulting sequence he determined is shown below. CCGGATCGGGTTTCCGGGAATCGGGGG Devonte asked his colleague George to verify his results by repeating the sequencing experiment in a different lab. George was disappointed to find that his gel showed just one DNA band with a fluorescently labeled “G.” What did he leave out of the sequencing mixture? a)Primer b)DNA polymerase c)All ddNTPs d)All dNTPs
1. How does PFGE separate larger fragments more efficiently than standard electrophoresis? 2. Why is SYBR green less toxic than EtBr? 3. What are the similarities and differences between Manual and Automated Sanger Sequencing? 4. What is the relationship between DNA fragment length and the distance it will run in a gel? (Restriction Enzyme Digestion)
Q No. 2 Describe sequence alignment. What kind of information do we obtain from pair wise or multiple sequence alignment? Also write down their applications in the field of bioinformatics. Enlist some softwares used to perform alignment. Plz write the answer with headings of sequence alignment Pair wise alignment Multiple sequence alignment And the name of softwares
Perform Progressive Alignment Method on the following 5 sequences and findthe best multiple sequence alignments.Sequence # 1: ATCCAATTTTSequence # 2: ACTGACCSequence # 3: ATGGCCATTSequence # 4: ATCTTCTTSequence # 5: ATTGCCATT
With regards to this sequence below please answer this quistions 1) What is the format of the sequence below and why 2) What do you understand by a query sequence 3) What is the sequence size of this sequence 4) What is the ID of the sequence and indicate the taxonomic rank of the ID ATGAAAAAACGAAAAGTGTTAATACCATTAATGGCATTGTCTACGATATTAGTTTCAAGCACAGGTAATT TAGAGGTGATTCAGGCAGAAGTTAAACAGGAGAACCGGTTATTAAATGAATCAGAATCAAGTTCCCAGGG GTTACTAGGATACTATTTTAGTGATTTGAATTTTCAAGCACCCATGGTGGTTACCTCTTCTACTACAGGG GATTTATCTATTCCTAGTTCTGATAGAAAATATTCCATCGGAAAACCAATATTTTCAATCTGCTATTTGG TCAGGATTTATCAAAGTTAAGAAGAGTGATGAATATACATTTGCTACTTCCGCTGATAATCATGTAACAA TGTGGGTAGATGACCAACAAGTGATTAATAAAGCTTCTAATTCTAACAAAATCAGATTAGAAAAAGGA AGATTATATCAAATAAAAATTCAATATCAACGAGAAAATCCTACTGAAAAAGGATTGGATTTCAAGTTGT ACTGGACCGATTCTCAAAATAAAAAAGAAGTGATTTCTAGTGATAACTTACAATTGCCAGAATTAAAACA AAAATCTTCGAACTCAAGAAAAAAGCGAAGTACAAGTGTGGACCTACGGTTCCAGACCGTGACAATGAT GGAATCCCTGATTCATTAGAGGTAGAAGGATATACGGTTGATGTCAAAAATAAAAGAACTTTTCTTTCAC…
Please answer ASAP RNA sequencing (RNA-Seq) of one sample in one run of a massively parallel sequencing platform is quite expensive. However, a way to circumvent this cost issue is to pool and sequence more than one sample. How would you be able to distinguish and identify the reads from different samples?
Objective: Get a sense of how genomics, the study of the genome in its entirety,needs to think about how to go about its research. Geonomic DNA is broken up into fragments. The 5’ and 3’ ends of each fragment(a “read”) are sequenced. The sequenced reads are assembled together intocontiguous sequences (“contigs”) based on sequence similarity. The idea is to sequence enough random fragments so that every nucleotide in thegenome is represented on some read. The number of such fragments needed iscalled the coverage, c. The coverage c can be calculated by the formula RL/G, where R is the number ofreads sequenced, L is the average length of a read and G is the total length of thegenome. The units of length are bases (b) or base pairs (bp). Consider a genome whose length is 1000 bp. “Shotgun” sequencing techniquesare applied to the genome, resulting in 20 reads, with an average length of 50 bp.A very important point is that, even though 20 x 50 = 1000, there is no guaranteethat ALL…
Objective: Get a sense of how genomics, the study of the genome in its entirety,needs to think about how to go about its research. Geonomic DNA is broken up into fragments. The 5’ and 3’ ends of each fragment(a “read”) are sequenced. The sequenced reads are assembled together intocontiguous sequences (“contigs”) based on sequence similarity. The idea is to sequence enough random fragments so that every nucleotide in thegenome is represented on some read. The number of such fragments needed iscalled the coverage, c. The coverage c can be calculated by the formula RL/G, where R is the number ofreads sequenced, L is the average length of a read and G is the total length of thegenome. The units of length are bases (b) or base pairs (bp). Consider a genome whose length is 1000 bp. “Shotgun” sequencing techniquesare applied to the genome, resulting in 20 reads, with an average length of 50 bp.A very important point is that, even though 20 x 50 = 1000, there is no guaranteethat ALL…
NGS sequencing made it easy to generate COVID-19 sequences and comparethem at different time points. Using what you learn in the course you are able to analyzeCOVID-19 data at different waves.Requirements1. Use the GISAID database (GISAID) to download COVID-19 sequences (at leastten samples) at different time points.2. Perform multiple sequence alignment for your samples.3. Generate a phylogenetic tree and visualize it.4. Use BLAST to align COVID-19 spike protein with other viral spike proteins.5. Choose the most homologous protein and annotate it using ensemble or anypreferred database.6. All analysis steps must be delivered in bash script
Examine the DNA sequence shown below. You have been tasked with designing Primers for PCR amplification of the whole fragment shown. Your colleague said that she would design one primer and came up with this sequence – 5’ TGCTATC 3’. You, being a good scientist, need to confirm that her work is good. Where will this primer bind on the target DNA? 5’ CGATGCAATCGAGCTATGGCATATCATAAGCGATAGACAGATAGCA 3’ GCTACGTTAGCTCGATACCGTATAGTATTCGCTATCTGTCTATCGT a. This primer cannot be used in the PCR process. b. It will bind to the top strand on the left side of the fragment. c. It will bind to the bottom strand on the left side of the fragment. d. It will bind to the bottom strand on the right side of the fragment. e. It will bind to the top strand on the right side of the fragment.
DNA ladder is attached (the picture shows HindIII as H, EcoRI as E, BamHI as B). Now, determine the size of fragments created by EcoRI and BamHI. In the graph attached there is the fragment size of HindIII. HindIII EcoRI BamHI Migration Distance (mm) Fragment Size (bp) Migration Distance (mm) Fragment Size (bp) Migration Distance (mm) Fragment Size (bp) 23455 11985 7430 4375 2150 1850