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

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

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

Database - UniProtKB

hemo_homo.fasta

Database - UniProtKB

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

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

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

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

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

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

Tool - BLAST 1. Known protein

Tool - BLAST 1. Known protein

Tool - BLAST 1. Known protein

Tool - BLAST 1. Known protein

Tool - BLAST 2. Unknown protein

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

Tool - BLAST 2. Unknown protein

Tool - BLAST 2. Unknown protein

Tool - BLAST 2. Unknown protein Unknown Protein aa

Tool - BLAST 2. Unknown protein

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

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

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

Now write the report The report should be sent to Prof. Neri Niccolai : and Simone Gardini :

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