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Analysis of Biomolecular Sequences 29/01/2015 Mail: Prof. Neri Niccolai Simone Gardini

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Presentation on theme: "Analysis of Biomolecular Sequences 29/01/2015 Mail: Prof. Neri Niccolai Simone Gardini"— Presentation transcript:

1 Analysis of Biomolecular Sequences 29/01/2015 Mail: Prof. Neri Niccolai Simone Gardini

2 Database - UniProtKB UniProtKB consists of two sections: Reviewed (Swiss-Prot, ) - Manually annotated Unreviewed (TrEMBL, ) - 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

4

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. Q )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 write your title copy and paste the link that arrives on your

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 : and Simone Gardini :


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