Elzu's micro notes

  Multiple Sequence Alignment using CLUSTAL W Aim To show phylogenetic relationships of sequences by creating tree. Description Multiple sequence alignment is simply an alignment that contains more than two sequences. Multiple sequence alignment is very important for finding similar domains in a set of sequences and further doing phylogenetic analysis. There are two methods of multiple sequence alignment; progressive and iterative. CLUSTAL W is an example of progressive method. It produces multiple sequence alignment of divergent sequences. Evolutionary relationships are shown through cladogram.   Procedure STEP 1: Obtain sequence from NCBI for multiple sequence alignment. Go to NCBI homepage, select nucleotide/protein database and type the query. Select the hit in FASTA format for similarity search. STEP 2: Select BLAST-n option from NCBI -BLAST STEP 3: Run BLAST. STEP 4: Select three or four sequence similar to query and download it in FASTA format. STE...

  RASMOL/RASWIN Show information and Background Aim To display information about the protein selected and to change the background color. Description RasMOL is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structure, such as those found in the protein data bank . It was originally developed by Ronger Dayle in the early 1990s.RasMOL includes a scripting language, to perform many functions such as selecting certain protein chains, changing colours etc. Jmol Sirus software have incorporated this language into their commands.   Procedure STEP 1: Open RasMol STEP 2: Open a new PDB file of protein Command RasMol.>Show information RasMol.>background white Output(take print) Result Information about the selected protein was displayed and background color was changed to white.               Show Sequenc...

  SNP Aim To retrieve single nucleotide polymorphism (SNP) of the given. Description Single nucleotide polymorphism frequently called SNPs, are the most common type of genetic variation among people. It is a variation in a single nucleotide that occurs at a specific positon in the genome .SNPs occur normally throughout a person’s DNA. They can act as a biological markers, helping scientists   to locate genes that are associated with disease. Procedure STEP 1: Open   https://www.ncbi.nlm.nih.gov/snp/ STEP 2: Select SNP from the dropdown list and type gene name in the search box and click on go. STEP 3: Select three hits from the displayed gene SNPs . STEP 4: Note down the accession number, chromosomal number, allele number and clinical significance. STEP 5: Save the page STEP 6: Close the window Result

  KEGG Aim To retrieve the “cysteine metabolism “ from Oryza savita Description KEGG (Koyoto Encyclopedia of Genes and Genomes ) is a database resource for understanding high level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from genomic and molecular level information. The most unique data object in KEGG is the molecular networks – molecular interaction, reaction and relation and relation networks representing systemic functions    of the cell and the organism .The KEGG database has been in development by Kanehisa Laboratories since 1995,and is now a prominent reference knowledge base for integration and interpretation of large –scale molecular sets generated by genome sequencing and other high-throughput experimental technologies. Procedure STEP 1: Access   https://www.genome.jp/kegg/ STEP 2: Select KEGG pathway STEP 3: Enter organism name and “cysteine metabolism” as keyword STEP 4: Click g...

  PIR Aim To retrieve aminoacid sequence for heat shock protein HSP70 in tomato. Description The protein information resource(PIR),located at Georgetown University Medical Center (GUMC), is an integrated public bioinformatics resource to support genomic   and proteomic research and scientific studies. PIR was established in 1984 by the National Biomedical Research Foundation(NBRF) as a resource to assist researchers and consumers in the identification and interpretation of protein sequence information. Prior to that ,the NBRF compiled the first comprehensive collection of macromolecular sequences n the Atlas of protein sequence and structure, published from 1964-1974,under the editorship of Margaret Dayhoff. Dr. Dayhoff and her research group pioneered in the development of computer methods for the comparison of protein sequences, for the detection of distantly related sequences and duplications within sequences and for the inference of evolutionary histories from al...

  DNA Data Bank of Japan  ( DDBJ ) Aim To retrieve information for a given organism from DDBJ Description DDBJ is a Primary nucleotide sequence database in Japan . The  DNA Data Bank of Japan  ( DDBJ ) is a  biological database  that collects DNA sequences. It is located at the  National Institute of Genetics  (NIG) in the  Shizuoka prefecture  of Japan. It is also a member of the  International Nucleotide Sequence Database Collaboration  or  INSDC . It exchanges its data with  European Molecular Biology Laboratory  at the  European Bioinformatics Institute  and with  GenBank  at the  National Center for Biotechnology Information  on a daily basis.   Presently, sequence submission to either GenBank, EMBL, or DDBJ is a precondition for publication in most scientific journals to ensure the fundamental molecular data to be made freely available.  Procedure ST...