Skip to main content

Search Tools

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 background hits that are found. From the work hits that are returned the program looks for the segments that contain a cluster of nearby hits. It then investigates these segments for a possible match. 
Image result for fasta example
Example of FASTA Format Result

b) BLAST: Basic Local Alignment Search Tool.. There are different types of BLAST. 

BLASTP = matches the protein query against protein database. 

BLASTN = matches the nucleotide query against nucleotide database.

BLASTX = matches 6 frame translated nucleotide query against protein database. 

TBLASTN = matches the protein query against translated (6 frame) nucleotide database. 

TBLASTX = matches the translated nucleotide query against translated nucleotide database. 

PSI-BLAST = Position Specific Iterative BLAST. A list of all closely related proteins is created. These proteins are combined into a general profile sequence, which summarizes significant features present in these sequences. A query against the protein database is then run using this profile, and a larger group of proteins is found. This large group is used to construct another profile. 

PHI-BLAST = Pattern Hit Initiated BLAST.
Labels:

Comments

Post a Comment

Popular posts from this blog

Statistics in Flow Cytometry Data and "MFI" values

                                 The speed of the flow cytometry offers wide range of data points and data plots. Due to its sensitivity and versatility, it has been used extensively. Flow cytometer can detect up to 1000s of cells per second.. But, it should be noted that the flow cytometry also involves the statistics, its significance, calculating the fluorescence intensity..                Statistics in flow cytometry involves, total number of data points acquired, percentage population, most importantly mean and median fluorescence intensity, and others. Most of us get confused about the term "MFI", whether it means mean fluorescence intensity or median fluorescence intensity.. Truth is, both.. It means it can be described as either mean or median fluorescence intensity. Some researchers use Mean for MFI and some use Median for MFI values.  (Keeping in mind that, consideration of statistics in flow cyomtery also depends on the type of Application you are interest
Post a Comment
....CONTINUE READING

Protocol: Chromosomal DNA Isolation from Bacteria

1.       Spin down 50-100 ml well-grown bacteria, 3600 rpm,15min. 2.     Resuspend bacteria with 20 ml Buffer S, immediately add 100 µl ProteinaseK (10 mg/ml). Vortex to make sure no chunks. 3.       Add 2 ml of 20% SDS, mix gently by inverting. 4.       Incubate the mixture at 65 o C for 1 hr with inverting every 15 min. 5.     Add 10 ml of phenol and 10 ml of chloroform, mix thoroughly by inverting for 5 min, spin at 3600 rpm for 20 min. 6.       Transfer supernatant to a new tube, add 0.6 volume of isopropanol. Mix gently by inverting. You will see cotton-like genomic DNA. 7.       Hook out the cotton-like DNA to a 1.5 ml tube; wash with cold 70% ethanol. 8.      Dry DNA at RT, dissolve DNA in 500 µl H 2 O (50 o C or 4 o C overnight). 9.      Add 5 µl DNase-free RNase A (20 mg/ml stock) to the DNA. Incubate at 37 o C for 30 min. 10.   Add 500 µl phenol, mix, spin at 3600 rpm for 20 min. Repeat phenol extraction once if necessary. 11.   Tr
Post a Comment
....CONTINUE READING

Gene Cloning Technique

Gene Cloning Technique in Molecular Biology Field Involves the following steps: 1.a) Isolation of Genetic Material and Gene Sequence of Interest.  First, cells are lysed using detergent or lysozyme enzymes which disrupts the plasma membrane and release the genetic material along with the macro molecules such proteins and RNA molecules. Cell contents are then treated with protease to disrupt the proteins and RNase to destroy the RNA. Cell debris are then pelleted using centrifuge and supernatant containing DNA is transferred to a fresh and clean tube. A proper amount of Ethanol is added to this supernatant and precipitated using centrifuge. Supernatant is discarded and the pellet which has DNA is suspended using a proper suitable buffer.  Primers are designed for the specific gene sequence of interest which will be used for the cloning procedure.  Gene sequence is then amplified using PCR (Polymerase Chain Reaction) which will yield in many copies of the gene sequence.
Post a Comment
....CONTINUE READING