BIOMAG

In bacteria, the Plasmid is present in the cytoplasm. To get the plasmid DNA out of the bacteria, its cell membranes must be disrupted in order to get the Plasmid DNA in the extraction buffer. There are three main solutions involves in the procedure.  Solution I : It contains Glucose, Tris and EDTA.. Glucose provides the Osmotic shock which leads to the disruption of the cell membrane. Tris  is buffering agent and maintains constant pH 8. EDTA is used to protect the Plasmid from endogenous nucleases by chelating the magnesium ions.  Solution II : it contains NaOH and SDS. This is an Alkaline solution. It is used to disrupt the cell and NaOH also denatures the DNA into single strands.  Solution III : it contains the acetic acid and potassium acetate. Acetic acid is used to neutralize the pH. and Potassium acetate is used to precipitate the chromosomal DNA, proteins and other cellular debris.  Phenol/Chloroform: It is used to denatu...

For building a phylogenetic tree, you need more than 2 sequences for both multiple sequence alignment and building a tree using ClustalW.  Phylogenetic Tree in bioinformatics represents the evolutionary relationship between species.  Follow these steps to build a tree: These steps are for building a phylogenetic tree for p53 of 4 different species (Homo sapiens, Mus musculus, Rattus norvegiccus, Danio rario). (You can consider the protein or dna of your interest to find the relationship between any number of species).  1) Go to NCBI homepage and select Nucleotide. And type in the search box "p53" and you will get number of hits for this query. And a number of entries for p53 in different species will be displayed. 2) Consider 4 different species (example: homo sapiens, mus musculus, rattus norvegiccus, danio rario). and retrieve FASTA format sequneces for those 4 species and paste them in a word file one by one.  3) Open https://www.e...

This is a practical experiment steps to carry out BLAST search of a given nucleotide sequence.   (You can either watch the video or go through the steps mentioned below the video).  Follow These Steps: Open NCBI home page http://www.ncbi.nlm.nih.gov/ Click on the text box which shows all databases and change it to "Nucleotide. In the search box, type name of a protein or gene whose sequence you would like to retrieve. For example: Human Insulin. Click on Home sapience at the right corner and you will get the list of all related Homo sapience.  Select whichever you want and click on it.  You will get the data in the format of Genbank. Since BLAST accepts only FASTA format, you need to change GenBank format to FASTA format by clicking FASTA. (just below the heading line).  The new page will appear where you will get the FASTA format of the nucleotide sequence.  Copy that sequence along with code present in the format. ...

Gene prediction is for the prediction and determining the coding and non-coding regions present in the given stretches of the sequence. For this, several gene prediction tools are used.  1) GENSCAN:  This tool can identify introns, exons, promoter sites and polyA signals. There are other gene prediction tools which do the same. It depends on what the user terms a "Probabilistic Model" of genome sequence composition and gene structure.  2) GRAIL:  It stands for Gene Recognition and Analysis Internet Link. GRAIL 1 makes use of a neural network method to recognize coding potential in a fixed length. GRAIL 1a expands on this method by considering regions immediately adjacent to coding regions.  3) FGENEH/FGENES:  FGENEH makes use of linear discriminant analysis which predicts the internal exons by looking for structural features such as donor and acceptor splices.  FGENES can be used when multiple genes are expected to ...

There are several techniques which are used for the identification of a protein structure such as optical rotatory dispersion, X-ray crystallography, spectroscopy and nuclear magnetic resonance, these techniques are powerful in determining the structural features of protein but they require many hours of highly skilled and technically dedicated work environments. There are several computational techniques which allow for the biological discovery based on the protein sequences only and/or on their comparison to protein families.  There are three main methods to identify protein and its structural features.  1) Protein Identity Based on Composition:  This involves the methods and online packages such as AA Compident, AA Compsim and Propsearch.. (AA stands for Amino Acid).  AA Compident: It uses the amino acid composition of the unknown protein to identify known proteins of the same composition.  AA Compsim: Instead of using the experimentally der...

Structure alignments are usually specific to protein sequences and RNA sequences. They provide the information about the secondary and tertiary structure of the protein or RNA molecule which will help in aligning the sequences more accurately.  a) DALI: It is a distance matrix alignment. It is a fragment based method for constructing structural alignments based on similarity patterns between successive hexapeptides in the query sequences. It can generate pair wise or multiple alignments and identify a query sequence's structural neighbors in the Protein Data Bank. b) SSAP: stands for Sequential Structure Alignment Program. It is a based on dynamic programming method of structural alignment that uses atom-to-atom vectors in structure space as comparison points.  Phylogenetic Analysis It refers to the studying of evolutionary relationships. Final goal is to construct the evolutionary tree describing the relationships of the various taxa with respect to each o...

There are two types of Search Tools in Bioinformatics. 1) Text Based Search Tools and 2) Sequence Similarity Based Search Tools.  1) Text Based Search Tools: a) SRS = Sequence Search and Retrieval Tool. PIR and other protein sequence database searching.  b) ENTREZ = This is for the nucleotide, GenBank, protein, DDBJ and NCBI searching. It is like a collection of these databases. c) ExPASy = stands for Expert Protein Analysis System, this is for the SWISS-PROT and other searching. 2) Sequence Similarity Based Search Tools: a) FASTA: This is a DNA and Protein sequence alignment online software package. This initially observes the word pattern hits, word-word matches of a given length, and matches the potential matches before performing more time consuming search using Smith-Waterman algorithm. The size taken for a work, given by the parameter ktup, controls the sensitivity, and speed of the program. Increasing the ktup value decreases the number of back...