Biostatistics and bioinformatics 4106.pptx

Biostatistics

1. Searching gene by using NCBI and HOMD Database Professor Dr. Md. Tanvir Sarwar Dept. Of Applied Nutrition and Food Technology Islamic University, Kushtia-7003, Bangladesh BIOINFORMTICS, ANFT- 4106 1

2. Gene 2

3. What is NCBI Database? The National Center for Biotechnology Information. It is a branch of the National Institutes of health (NIH). The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed 3

4. GenBank GenBank is a public, comprehensive database of publicly available DNA and RNA sequences, along with their supporting biological and bibliographic information 4

5. Searching gene by NCBI database NCBI The NCBI database refers to the entire suite of databases and informational resources provided by the National Center for Biotechnology Information (NCBI), a U.S. government-funded institution within the National Library of Medicine (part of the National Institutes of Health). 5

6. Title- 1 Search human ACE gene from NCBI database and present in FASTA format Step- 1, Type NCBI database on Google Search Step- 2 6

7. Step- 3 Step- 4 7

8. Step- 5, Type ACE in the search box Step- 6, Now click on search and you will get the following results 8

9. Step- 7 Step- 8, at the bottom of the page you will get the following info about the gene 9

10. Step- 9 Step- 10 10

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12. 12 Alternatively you can go down to the page and click on FASTA to get FASTA sequence of the gene

13. 13 N is almost absent here because it is perfectly sequenced version of the gene

14. Tasks for you Search and describe gene SR187_RS09630 Search and describe gene rgpB Search and describe gene PGN_RS01405 Search and describe gene Mfa4 Search for the gene responsible to code SRPBCC family protein [ Streptococcus intermedius ] and describe it Search for the gene responsible to code S8 family serine peptidase [ Streptococcus  ruminantium ] 14

15. Title- 2 Search Porphyromonas gingivalis W83, complete genome from HOMD database and present in FASTA format Step- 1 Step- 2 15

16. Step- 3, Select P from alphabet and go don to the list..... Step- 4, Now click on genome info of PgW83 16

17. Step- 4, Click on G enBank Assembly ID and rest of the search is same as NCBI.... 17

18. Tasks for you Find the whole genome seq of Parvimonas micra EYE_25 Find the whole genome seq of Parvimonas micra EYE_25 Tannerella forsythia WW11663 Treponema denticola AL-2 Bacillus anthracis A0442 Bacillus anthracis H9401 18

19. Title- 3 Perform multiple sequence alignment by CLUSTALW CLUSTALW is a widely used, general-purpose software program for creating multiple sequence alignments of DNA or protein sequences. Its primary function is to align several homologous (evolutionarily related) sequences simultaneously to identify similarities and differences 19

20. Find sequence similarities between PGN_RS08215 and PGN_RS08440 gene sequence 20

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25. Tasks for you Compare the gene similarity between SR187_RS01870 and BLR40_RS05460 Compare the gene similarity between C5a peptidase ScpA/B [ Streptococcus agalactiae ] and S8 family serine peptidase [ Streptococcus  equinus ] oligoendopeptidase F [ Streptococcus  pseudoporcinus ] and oligoendopeptidase F [ Halalkalicoccus jeotgali B3 ] scpA /B and scpC SR187_RS01870 and scpC CXC chemokine -degrading serine protease SpyCEP scpA /B and SR187_RS01870 25