Biological Sequence Database,Bsc Botany 5th sem DSE4 Notes Bioinformatics

  

আজিৰ এই পষ্টটোত ,যেতিয়া উদ্ভিদ বিজ্ঞান বিভাগত পঢ়ি আছিলো আৰু তেতিয়া বনাইছিলো পৰীক্ষাৰ বাবে নোট সেয়ে এই পষ্টটোত  মোৰ নোটৰ কিছু কালাংশ DTP কৰি পষ্ট কৰি দিলো।ইয়াৰ কিছু সংখ্য ইন্টাৰনেটৰ সহায়ত বনোৱা হৈছে/when I was studying in the Department of Botany and then I made notes for the exam so I posted some excerpts of my note in this post 

   Unite 3: Biological Sequence Database

1.What is BLAST? How many types  of BLAST ?

Ans:-Blast is a set of sequence comparision algorithm use to such  database  for optional local alignment to query. The full from of BLAST is local Alignment search tool .It  as breaks query and databases sequence into fragment and matches between them.
Types of  BLAST :-   BLAST  is divided into six types-
(a).BLAST-n(Nucleotide BLAST) :-Compares one or more nucleotide query sequence to  a subject nucleotide  query sequence to a subject nucleotide sequence to or  database of nucleotide sequence .This is useful when trying to determining the evolutionary  relationships among different organisms.
(b)BLAST-X(Trsanslocated nucleotide sequence searched against proteins sequence) :- Compares a nucleotide query sequence that is translocated in six reading .Because BLAST-X translocates the query sequence in all six reading frames and provides combined significance statistics fo different from it is particul.Only useful when  the reading framshifts or other coding errors.
(c)BLAST-P :- This is programme given a protein queiry refers the most similar protein queiry refers the most similar protein sequence from the protein database.
(d)PSI-BLAST:-This programme compares the six conceptual translocation for the nucleotype query.
(e)t-BLAST-X – This programme  uset to find out very distant relationship between nucleotype sequence.
(f)Mega-BLAST – This programme has been use for company large number input sequence higher the comman BLAST.
                       Above mention type BLAST-N,BLAST B and other most commonly they used comparison and dono equally translocation.

Uses of BLAST

(i).Identification of species.
(ii).Stability transogenic
(iii)DNA trapping.
(iv).Comparison of DNA.

2.Explain the sequence of “Protein Sequence Database”

Ans:  The Database in which amino acid sequence in of protein are stored is known of Protein Sequence Database.There are many different protein sequence  database to assist the research in  getting amino acid sequence of different  proteins.example Exprot,NCBI protein Database PIR,Swiss-Prot,TrEMBL and UnitProt are some important protein sequence database.
PIR-Proteib Information Resources ,which database  tool as https://yearyebms.edu iprred class. PIR database is an outgrowth of the protein sequence database originally created by  murgarator deaf .It is Currently main collaboration  with munich information centre for proteinsequence Germany(MTPS) and the Japanese international   proteins  database.

3.Write the short notes on  about  of “Resourse of PIR”.

Ans: The Proteins Information Resources (PIR) produces the largest ,Most comprehensive  annoted protein sequence database in the public domain,the   PIR –International with Munich Infromation center for  protein sequence and the Japanese International Protein Sequence database.
              Resource of PIR the can be broadly classified into two types-
(i)Data Retrival System.
(ii)Databasae.

4.Write the  salient feature with Descriptive to Nucleotide Sequence Database ?

Ans :- Nucleotide Sequence Database :  The database in which sequence of data of DNA  ,CDNA ,MRNA and TRNA are stored is said to be nucleotide sequence database.Nucleotide sequence data  are given  in the database as they were originally submitted to the database or appeared in  the paper.

Salient feature of Nucleotide Sequence Database

i.Sequence are present in a form as they are in the biological  invivo.
ii.c DNA  Sequence are considered as RNA sequences are considered as RNA sequence.
iii.For genomic DNA only coding strand is stored.
iv.The sequence data generally correspond to  wild type individuals.
v.t RNA sequences are stored as unmodified RNA sequences for easily storage and analysis.
 

4.Write the Introduction and Salient feature of Swiss-Prot ?

Ans – Introduction of Swiss-Prot :- Swiss-Prott is an annotal protein sequence database .It was established by Amos Bairoch at the department of medical Biochemistry at the university of Geneva in 1986.It was maintained collaborately by Swiss-Prot.Institute of Bio-Chemistrys (SIB) and Eurpean Bioinformatics Institute(EBI) since 1987.It is available at the website https://www.expasy.ch/spro/.  This database is generally considered one of the best protein sequence database in term of the quality of the annotation.

                      This Swiss-Prot database has some legal restriction, the entries themselves are copyrighted ,but freely accessible and usable by academic resarchs.

Salient features of Swiss-Prot :

i.Computer amino acids sequence of stored protein are included .
ii.Taxonomic data of source organisms are given.
iii.Functions of the protein are mentioned.
iv.Post-Transcriptionsl modification with carbohydreates ,phosphate groups,actyle group ,metal ,GPI anchor –etc.are given.
v.Quarternarty structure is explained well.
vi.Disease associated with the protein are mentioned property.