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Dna Sequence

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Submitted By amsquared
Words 2349
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INDEX
1.To retrieve the protein or DNA sequence in FASTA format from the NCBI database and analyze the obtained data.
2.For a given protein sequences find the function ,structural relevance and annotation studies by using Uniprot/Uniprot KB.
3.For a given protein, find the protein PDB code ,release date , resolution ,Classification and pub med citation from PDB Structure data base.
4.Find the disease pathway ,drug target enzymes and drug molecules used for a given disease by using KEGG database.
5.For a given protein/enzyme find its EC number ,its location and Km, K cat/Km values by using BRENDA/KEGG database.
6.Find the pair wise sequence alignment for a given protein/DNA sequence by using Dot matrix method Dot helix and comment on the results inverted repeats ,palindromes.
7.For a given Protein sequence find the homolog sequences and Study the obtained output critical statistical parameters, the % identity, %similarity ,p ,E-value by using BLAST.
8.For a given Protein/DNA sequence find the pblast ,nblast ,psi blast ,phi blast ,blast, tbalstn and analyze the obtained results obtained results for each blast method.
9.For a given Protein sequence find the pair wise sequence alignment by using the FASTA algorithm and compare the results obtained with those from other methods.
10.Find the optimal alignment for the given protein sequence by using Dynamic programming –LALIGN method.
11.For a given FASTA sequence find the multiple sequence alignment by using the Clustal W/T-coffee and find the conserved regions ,motifs and profiles.
12.Find the motifs/domains for a given protein sequences by using Web logo program.
13.Construct the Phylogenetic Trees for the given sequences using MEGA. 1) Distance based method. 2)Maximum Parsimony method. 3)Maximum Likelihood method.

EXPERIMENT- 1
AIM :To Retrieve the protein or DNA sequence in FASTA format from the NCBI database and analyze the obtained data.
SOFTWARE USED : internet access,NCBI data base.
PROCEDURE:
STEP 1 : Open web browser and type the web address of the required NCBI database.
STEP 2 : Explore the database and analyze the various information available for PROTEIN or DNA sequence in the database.
STEP 3 : Save the output into a separate folder in FASTA format.
OUTPUT :

The file format of the particular protein keratin can be shown follow:

FASTA format :

RESULT: obtained the protein or DNA sequence in FASTA format from the NCBI database.

EXPERIMENT- 2
AIM: For a given protein sequence find the function, structural relevance and annotation studies by using Uniprot / UniprotKB.
SOFTWARE USED : internet access.
PROCEDURE:
STEP 1: Open Uniprot Database www.unitprot.org.
STEP 2:Enter the protein Id in search tab and click on Find.
STEP 3:Click on the protein name displayed on the result page.
STEP 4:Observe the protein function and structural information of protein sequence.
OUTPUT:

RESULT: observe for a given protein sequence function ,structural revelance and annotation by using Uniprot/Uniprot KB.

EXPERIMENT- 3
AIM :For a given protein find the protein PDB code ,release date ,resolution ,classification and pub med ,citation from PDB structure database.
SOFTWARE USED : internet access, PDB data base
PROCEDURE:
STEP 1: Open PDB Database www.pdb.org.
STEP 2:Enter the protein Id or molecule name or author name in search tab and click on Find.
STEP 3:Click on the relevant PDB code displayed on the result page.
STEP 4: Click on the code and display the release date, resolution of the protein , Primary Citation ,molecular description of the protein .Observe the protein functions and 3D structural information of protein in pdb database.
STEP 5:Download the protein sequence in PDB file format and save it.
OUTPUT:

Molecular Description of the protein:

Primary citation of the protein:

PDB file format: RESULT and CONCLUSION: Obtained the 3D structure of the given protein, analyze the functions of the protein.

EXPERIMENT- 4
AIM :Find the disease pathway ,drug target enzymes and drug molecules used for a given disease by using KEGG database
SOFTWARE USED : internet access ,KEGG database.
KEGG : Kyoto Encyclopedia of Genes &Genomes .
KEGG is a path-way database resource for understanding high-level functions and utilities of the biological system, such as the cell ,the organism and the ecosystem ,from molecular-level information ,especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies. The information in KEGG is maintained manually.
PROCEDURE:
Step 1:Open KEGG database and select KEGG pathway option and mention the enzyme name from there we can get the pathway of disease and other related information.
KEGG:

KEGG pathway:

RESULT and CONCLUSION : Thus human diseases ,drug development ,genetic information processing, environmental information processing and representing metabolism processing is understood by KEGG path way.

EXPERIMENT- 5
AIM: For a given protein/enzyme find its EC number ,its location and Km, K cat/Km values by using BRENDA/KEGG database.
SOFTWARE USED : internet access , BRENDA/KEGG database.
BRENDA :BRauns chweig Enzyme Database It is an enzyme specific database maintained and developed at the Institute of Biochemistry and Bioinformatics at the Technical University of Braunschweig, Germany. The database is built on a relational database of molecular and metabolic information
PROCEDURE:
Step 1:Go to BRENDA enzyme database.
Step 2:In BRENDA home page consisting of EC number, enzyme name, organism ,protein, ligand advanced search.
Step 3:Then enter the enzyme name in query box.
Step 4:After given the query enzyme name then displays the Recommended names ,synonyms and particular EC numbers.
Step 5: Click on to the particular EC numbers, displays the regarded information about the enzymes.
Output:
BRENDA home page:

RESULT OBTAINED FOR A PARTICULAR ENZYME:

RESULT and CONCLUSION :EC number ,its location and km, k cat values of a given protein is thus obtained by using BRENDA data base.

EXPERIMENT- 6
AIM :Find the pair wise sequence alignment for a given protein/DNA sequence by using Dot matrix method Dothelix and comment on the results inverted repeats, palindromes.
SOFTWARE USED : internet access.
PROCEDURE:
STEP 1:. The program requires two nucleic acid sequences(FASTA sequences), which can be pasted into the text boxes labeled DNA Number 1 and DNA Number 2.
STEP 2: After filling each text box with a sequence and setting window size and mismatch limit.
STEP 3: click the Plot button. Note that all messages, including error alerts, are displayed in the yellow text box.
STEP 4: Once a plot is generated, clicking on a point within it will generate a message describing the relative position (base number) in the two sequences.
STEP 5:If the two sequences are identical then the dot plot is diagonal and observe the repeated regions.
STEP 6: If the two sequences are complementary each other then the dot plot is inverted diagonal and observe the repeated regions.
Output:
Two sequences are identical :

If the two sequences are complementary each other:

RESULT: Observe the plot ,if two sequences are then the dot plot is diagonal and if the two sequences are complementary each other then the dot plot is inverted diagonal.

EXPERIMENT- 7 |
AIM :For a given protein sequence find the homolog sequences and study the obtained output critical statistical parameters ,the % identity, % similarity ,P,E-values by using BLAST.
SOFTWARE USED : internet access.
PROCEDURE:
Step 1: Select the BLAST program.User have to specify the type of BLAST programs from the database like BLASTp, BLASTn, BLASTx, tBLASTn, tBLASTx.
Step 2: Enter a query sequence or upload a file containing sequence.Enter a query sequence by pasting the sequence in the query box or uploading a FASTA file which is having the sequence for similarity search. This step is similar for all BLAST programs. The user can give the accession number or gi number or even a raw FASTA sequence. Go to simulator tab to know more about how to retrieve query sequence. Step 3: Select the database to search. User first has to know what all databases are available and what type of sequences are present in those databases. Sequence similarity search involves searchin g of similar sequences of the query sequence from the selected databases . Step 4: Select the algorithm and the parameters of the algorithm for the search.
Step 5: Run the BLAST program.
Output:

Homology sequences for a given protein sequence:

RESULT: Observe the homolog sequences for a given protein sequence, and also observe the %similarity,% identity,E- value.

EXPERIMENT- 8 |
AIM :For a given protein/DNA sequence find the pblast, nblast, psi blast,phi blast,tblast and analyze the obtained results for each blast method.
SOFTWARE USED : internet access.
PROCEDURE:
Step 1: Select the required database that is PROTEIN DATABASES .
Step 2: Enter your input sequence .Enter or paste a PROTEIN sequence in any supported format.
Step 3: Set the default parameters . Expect: 1,The Expect value for inclusion in PSI-BLAST iteration 1: 0.001 Bottom of Form Filter Low complexity. BLOSUM62. Top of Form
Step 4:Submit the data and perform the psi blast (first iteration).
Step 5:Repeat above procedure.
Output:

Homolog sequences for a given sequences: Remote Homolog sequences for a given sequences: RESULT:By using the psi blasr we can identify the homolog sequences(that is100% similarity) and remote homologs (less than 30% similarity) in a given sequence.

EXPERIMENT- 9 |
AIM :For a given protein sequence find the pair wise sequences alignment by using the FASTA algorithm and compare the results obtained output with those from other methods .
TOOLS REQUIRED: internet access ,fasta database.
PROCEDURE:
STEP 1:Specify the tool input. Select the database to search :Databases are required to run the sequence similarity search. Multiple databases can be used at the same time. The different databases are Uniprot Knoweldge base Uniprot KB/swiss-prot Uniprot KB/ Swissprot isoforms Uniprot KB /Trembl UniProtKB Taxonomic Subsets UniProt Clusters Step 2 :Entering of input sequence.The query sequence can be entered directly in GCG, FASTA, EMBL, GenBank, PIR, NBRF, PHYLIP or UniProtKB Step 3: Setting up parameters.User has to specify the type of program and the matrix for scoring. FASTA, FASTX, FASTY, SSEARCH, GGSEARCH and GLSEARCH are the different programs used. Substitution matrix are used for scoring alignments. The matrices are BLOSUM50, BLOSUM62, BLASTP62, PAM120, PAM250, MDM10, MDM20, and MDM40. BLOSUM50 is set as a default substitution matrix. Parameters include.

Step 4: Submission.The result page can be seen in another window by clicking submit. This is an interactive process, when the process is complete the result will be displayed in the browser. Result can be sent to a valid email address which has to be specified in the text box.

FASTA Result Analysis:Result page appears by giving the information like aligned sequences fromthe sequence similarity search, database id, source of the sequence, Gene-expression, molecule type,Nucleotide sequence, Genomics, Protein sequences, Ontologies, Enzymes, protein families, and Literature, which is followed by the length of sequence, score, identities, positives and E-value.

Tool output:Tool output gives complete statistical details of the sequence similarity search.

Visual output: FASTA visual output gives the result of the sequence match and subject match with their E-values in a colour full schem. CONCLUSION: Pair wise sequence alignment of protein sequence by using FASTA algorithm and comparing this result with other methods is obtained.

EXPERIMENT- 10
AIM :Find the optimal alignment for the given protein sequence by using Dynamic programming –LALIGN method.
TOOLS REQUIRED: internet access .
PROCEDURE:
Step 1 : Enter protein sequences. Enter or paste your first protein sequence in any supported format.
Step 2: AND Enter or paste your second protein sequence in any supported format.
Step 3: Set default settings in pair wise alignment options.
Step 4: Submit the alignment .
Step 5:Display the alignment output identify,the identies,conservative replacements,non conservative replacements and observe the alignment file
OUTPUT:

Visual output: Conclusion: Observe the optimal alignment by using the Lalign method for the given protein sequences.

EXPERIMENT- 11
AIM :For a given protein FASTA sequence find the multiple sequence alignment using the Clustal W/T-coffee and find the conserved regions, motifs and profiles.
TOOLS REQUIRED: internet access , Clustal W/X,T-coffee .
PROCEDURE:
Step 1 : Open Clustal X/W or T-coffee and load the FASTA sequences taken from primary databases which has to be aligned and perform alignment .Enter protein sequences. Enter or paste your first protein sequence in any supported format.
Step 2: Set your Pair wise Alignment Options.
Step 3: Set your Multiple Sequence Alignment Options
Step 4: Submit the alignment .
OUTPUT:
T-coffee:

Clustal W:

RESULT AND CONCLUSION :Getting the Multiple Sequence alignment from which can observe the Conserved regions, Motif and Domains .Identify the positions of the residues where the conserved regions occur to get the functional similarities also.

EXPERIMENT- 12
AIM :Find the MOTIFS/DOMAINS for the given protein sequence by using MAST/Weblogo program.
TOOLS REQUIRED: internet access .
PROCEDURE:
Step 1 :Open Clustal/T-coffee and do the multiple sequence alignment for the given sequences.Save the result in the clustal format.
Step 2: Open the web logo website.
Step 3: Enter or upload protein sequences data or browse the sequence file in query boxes.Set the default settings.
Step 4: Then click the create logo button.
Output:

SEQUENCE LOGO :

RESULT AND CONCLUSION: Sequence logo/web logo is created for the aligned sequences .By observing the logo can identify the Conserved regions by observing the residue sizes .If the size is high then the residue occurrence is more and vice-versa.

EXPERIMENT- 13
AIM : Construct the Phylogenetic Trees for the given sequences using MEGA. 1) Distance based method. 2)Maximum Parsimony method. AND Maximum Likelihood method
TOOLS REQUIRED: internet access ,clustal ,Mega.
PROCEDURE:
Step 1: Perform the Multiple Sequence alignment of the given sequences and save the result in the clustal format.
Step 2: Open MEGA and select the Phylogeny option and select the type of construction method and can construct the tree.
Output:

UPGMA-method :

NJ-method:
Maximum Parsimony-method:

Maximum Likelihood-method:

Bootstrapping:

RESULT and CONCLUSION :Constructing the trees by different methods and getting the evolutionary relations and the distances between the given sequences .And observe the different construction trees.

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...TUTORIAL 3 SEQUENCES AND SERIES 3.1 Sequences and Series 1. Find the first four terms and 100th term of the sequence. (a) [pic] (b) [pic] (c) [pic] 2. Find the nth term of a sequence whose first several terms are given. (a) [pic]…… (b) 0, 2, 0, 2, 0, 2 …… 3. Find the sum. (a) [pic] (b) [pic] 4. Write the sum using sigma notation. (a) [pic] (b)[pic] 5. Find the nth term for each of the following sequences. Hence, determine whether the respective sequence is divergent or convergent. For a convergent sequence, state its limits. [pic] [pic] 6. For the sequence [pic]find the nth term and show that the above sequence is convergent and determine its limits. 7. The tenth term of an arithmetic sequence is [pic], and the second term is [pic]. Find the first term. 8. The first term of an arithmetic sequence is 1, and the common difference is 4. Is 11937 a term of this sequence? If so, which term is it? 9. The common ratio in a geometric sequence is [pic], and the fourth term is [pic]. Find the third term. 10. Which term of the geometric sequence 2, 6, 18, … is 118098? 11. Express the repeating decimal as fraction. (a) 0.777… (b) [pic] (c) [pic] 12. Find the sum of the first ten terms of the sequence. [pic] 13. The sum of the first three terms of a geometric series is 52, and the common ratio is r = 3. Find the first term. 14. A person has two parents, four grandparents, eight great-grandparents,...

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College Math Ii

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Test of Control

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