In Silico Structural and Functional Annotation of Hypothetical Protein Full Project Bangla Tutorial

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Hypothetical Protein: • A hypothetical protein is a protein whose existence has been predicted, but for which there is a lack of experimental evidence that it is expressed in vivo. Sequencing of several genomes has resulted in numerous predicted open reading frames to which functions cannot be readily assigned. These proteins, either orphan or conserved hypothetical proteins, make up ~ 20% to 40% of proteins encoded in each newly sequenced genome. Even when there is enough evidence that the product of the gene is expressed, by techniques such as microarray and mass-spectrometry, it is difficult to assign a function to it given its lack of identity to protein sequences with annotated biochemical function. Nowadays, most protein sequences are inferred from computational analysis of genomic DNA sequences. Hypothetical proteins are created by gene prediction software during genome analysis. When the bioinformatic tool used for the gene identification finds a large open reading frame without a characterized homolog in the protein database, it returns hypothetical protein as an annotation remark. • In Silico Structural and Functional Annotation of Hypothetical Proteins • 1. Sequence Retrieval – Download FASTA of Target Protein (NCBI-https://www.ncbi.nlm.nih.gov/protein) • 2. Determination of Physicochemical Properties (Protparam-https://web.expasy.org/protparam/ ) • 3. Subcellular Localization (Cello- http://cello.life.nctu.edu.tw/ ) • 4. Function Predictions (NCBI- Conserved Domain- https://www.ncbi.nlm.nih.gov/Structur... ) • 5. Homology Searching (PBLAST- https://blast.ncbi.nlm.nih.gov/Blast.cgi ) • 6. Multiple Sequence Alignment (Clustal Omega- https://www.ebi.ac.uk/Tools/msa/clust... ) • 7. Phylogenetic Tree Prediction (Clustal Omega) • 8. Secondary Structure Prediction (PSIPRED- http://bioinf.cs.ucl.ac.uk/psipred/, SOPMA- https://npsa-prabi.ibcp.fr/cgi-bin/np... ) • 9. Tertiary Structure Prediction (SWISS-Model- https://swissmodel.expasy.org/ ) • 10. Tertiary Structure Validation (PROCHECK- https://saves.mbi.ucla.edu/, ProSA-web - https://prosa.services.came.sbg.ac.at... )

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