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Es 243 Biology For Engineers Assignment-2: Question-1

1. The document is a biology assignment containing 10 questions. 2. It discusses global and local pairwise sequence alignment algorithms Needleman-Wunsch and Smith-Waterman. 3. It also examines how the Protein Data Bank and National Center for Biotechnology Information align with FAIR data principles of findability, accessibility, interoperability, and reusability.

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20 views

Es 243 Biology For Engineers Assignment-2: Question-1

1. The document is a biology assignment containing 10 questions. 2. It discusses global and local pairwise sequence alignment algorithms Needleman-Wunsch and Smith-Waterman. 3. It also examines how the Protein Data Bank and National Center for Biotechnology Information align with FAIR data principles of findability, accessibility, interoperability, and reusability.

Uploaded by

kum.joe.69
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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ES 243 BIOLOGY FOR ENGINEERS

ASSIGNMENT-2

Nikhil Kumar Lal 22110167

QUESTION-1
QUESTION-2

Refseq transcripts(26)

Refseq Proteins(25)

RefseqGene (1)
QUESTION-3
FOR NEEDLE-
https://www.ebi.ac.uk/Tools/services/web/toolresult.ebi?jobId=emboss
_needle-I20231117-165701-0424-82361430-p1m

FOR WATER
QUESTION-4

For Needleman Wusch: Affinity Gap penalty is used in this algorithm which is also called Global
pairwise alignment. Below parameters are used :
Gap open= 10
Gap extend=0.5
For Smith-Waterman: Affinity Gap penalty is used in this algorithm which is also called Local
pairwise alignment. Below parameters are used :
Gap Open=10
Gap extend=0.5
QUESTION-5
QUESTION-6
QUESTION-7
QUESTION-8
QUESTION-9
QUESTION-10

The FAIR data principles (Findable, Accessible, Interoperable, and Reusable) provide
guidelines for enhancing the usability of digital assets, including scientific data. The principles
are designed to improve the discoverability and accessibility of data, as well as promote
interoperability and reusability. As of my last knowledge update in January 2022, both the
Protein Data Bank (PDB) and the National Center for Biotechnology Information (NCBI) have
made efforts to align with FAIR data principles, but it's essential to note that specific practices
may evolve over time.
​ Protein Data Bank (PDB):
● PDB has taken steps to enhance the findability and accessibility of data. The
PDB archive provides a user-friendly interface for searching and retrieving
structural data of biological macromolecules.
● PDB identifiers (PDB IDs) serve as unique and persistent identifiers for each
entry, contributing to the findability of the data.
● Efforts have been made to make data interoperable, and PDB format standards
facilitate the exchange of structural information.
​ To obtain the most current and specific information, it is advisable to check the latest
documentation and statements from the PDB.
​ National Center for Biotechnology Information (NCBI):
● NCBI is committed to making biological data findable and accessible. Databases
such as GenBank, PubMed, and others hosted by NCBI aim to provide a wealth
of biological information.
● The use of unique identifiers (e.g., accession numbers) contributes to the
findability of biological data in NCBI databases.
● NCBI also promotes interoperability by providing various tools and resources that
enable users to link and integrate data from different NCBI databases.
​ As with any organization, practices may change over time, and it's advisable to consult
the latest documentation and policies from NCBI for the most up-to-date information.
For the latest and most accurate information regarding FAIR data principles adherence by PDB
and NCBI, it is recommended to visit their official websites or contact the respective
organizations directly.

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