1. Analysis of Biomolecular Sequences 29/01/2015 Mail: Prof. Neri Niccolai neri.niccolai@unisi.it Simone Gardini simone_gardini@hotmail.com http://www.sienabiografix.it/index_edu.php

2. Database - UniProtKB UniProtKB consists of two sections: Reviewed (Swiss-Prot, 547 357) - Manually annotated Unreviewed (TrEMBL, 89 4511 66) - Computationally analyzed The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. Universal Protein Resource

3. Database - UniProtKB

5. hemo_homo.fasta

6. Database - UniProtKB

7. 1)How many proteins found if you look for Rna Polymerase of Ebola? Questions

8. Database - UniProtKB 2)Save all sequence in FASTA format into a file (Surname.fasta) Questions

9. Database - UniProtKB 3)Save one sequence in FASTA format into a file (UniProt ID = Entry, save as UniprotID.fasta) Questions

10. Database - UniProtKB 4)Which domains found for that protein? (UniProt ID -> NUM) Questions

11. Database - UniProtKB 5)Title, Author and Year of first article for the protein choice Questions

12. Tool - BLAST BLAST is a method to ascertain sequence similarity. BLAST is a suite of programs provided by NCBI for aligning query sequences against those present in a selected target database. The results are reported in a form of a ranked list followed by a series of individual sequence alignments, plus various statistics and scores. Two methods for using Blast: 1.Known protein 2.Unknown protein Basic Local Alignment Search Tool

13. Tool - BLAST 1. Known protein

14. Tool - BLAST 1. Known protein

15. Tool - BLAST 1. Known protein

16. Tool - BLAST 1. Known protein

17. Tool - BLAST 2. Unknown protein

18. Tool - BLAST 2. Unknown protein MDGSGEQPRGGGPTSSEQIMKTGALLLQGFIQDRAGRMGGEAPELALDPVPQ DASTKKLSCLKRIGDELDSNMELQRMIAAVDTDSPREVFFRVAADMFSDGNFN WGRVVALFYFASKLLKALCTKVPELIRTIMGWTLDFLRERLLGWIQDQGGWDG LLSYFGTPTWQTVTIFVAGV LTASLTIWKKMG

19. Tool - BLAST 2. Unknown protein

20. Tool - BLAST 2. Unknown protein

21. Tool - BLAST 2. Unknown protein Unknown Protein aa

22. Tool - BLAST 2. Unknown protein

23. Tool – BLAST from UniProt 1)For this protein using the tool blast A.Q8JPX5B. Q6V1Q2 C. Q66802 2)How many known structures found? 3)Write UniProt ID, Name and Organism of the protein with sequence identity lower 4)Save all protein in FASTA format (save as Blast_surname.fasta) Questions

24. Tool – CLUSTAL OMEGA Save results write your email write your title copy and paste the link that arrives on your email

25. Tool – CLUSTAL OMEGA Questions 1)Align all proteins found with UniProt (Rna Pol Ebola) 2)Save results 3)Align all proteins reviewed found with BLAST 4)Save results

26. Now write the report The report should be sent to Prof. Neri Niccolai : neri.niccolai@gmail.com and Simone Gardini : simone_gardini@hotmail.com