Proteogenomics and Gene Annotation
Introduction
Proteogenomics is a kind of science field that includes proteomics and genomics. Proteomic consists of protein sequence information and genomic consists of genome sequence information. It is used to annotate whole genome and protein coding genes. Proteomic data provides genome analysis by showing genome annotation and using of peptides that is gained from expressed proteins and it can be used to correct coding regions.Identities of protein coding regions in terms of function and sequence is more important than nucleotide sequences because protein coding genes have more function in a cell than other nucleotide sequences. Genome annotation process includes all experimental and computational stages.These stages can be identification of a gene ,function and structure of a gene and coding region locations.To carry out these processes, ab initio gene prediction methods can be used to predict exon and splice sites. Annotation of protein coding genes is very time consuming process ,therefore gene prediction methods are used for genome annotations. Some web site programs provides these genome annotations such as NCBI and Ensembl. These tools shows sequenced genomes and gives more accurate gene annotations. However, these tools may not explain the presence of a protein. Main idea of proteogenomic methods is to identify peptides in samples by using these tools and also with the help of mass spectrometry.Mass spectrometry searches translation of genome sequences rather than protein database searching. This method also annotate protein protein interactions.MS/MS data searching against translation of genome can determine and identify peptide sequences.Thus genome data can be understood by using genomic and transcriptomic information with this proteogenomic methods and tools. Many of proteomic information can be achieved by gene prediction algorithms, cDNA sequences and comparative genomics. Large proteomic datasets can be gained by peptide mass spectrophotometry for proteogenomics because it uses proteomic data to annotate genome. If there is genome sequence data for an organism or closely related genomes are present,proteogenomic tools can be used. Gained proteogenomic data provides comparing of these data between many related species and shows homology relationships among many species proteins to make annotations with high accuracy.From these studies, proteogenomic data demonstrates frame shifts regions, gene start sites and exon and intron boundaries , alternative splicing sites and its detection , proteolytic sites that is found in proteins, prediction of genes and post translational modification sites for protein.
Protein extractions from unidentified fish samples were separated according to the molecular weights by SDS polyacrylamide gel electrophoresis. Since some of these proteins are shared between fishes, phylogenetic evaluation was reached. Western blot analysis was used to identify four unknown species of aquatic animals via comparison of actin/myosin bands. According to the results of this assay, the best estimate is that the unidentified aquatic animals are specimens of salmon, tilapia, cod, and shrimp, respectively. Introduction Western blot has been a revolutionary technique for identifying the expression of proteins within relative molecular biological samples that shared the same ancestor.
...It allowed access to virtually annotate sequences freely, build and visualize maps, design primers, and restriction analysis. First, the pEGFP-N1 plasmid nucleotide sequence was found by using the NCBI nucleotide database program. SnapGene viewer illustrated the restriction enzyme cut sites used to cut EGFP gene from the pEGFP-N1 source plasmid. Then the pET-41a (+) vector sequence was found by using the AddGene Vector Database. A new DNA file representing the recombinant pET-41a (+)-EGFP plasmid was built by virtually cloning the EGFP gene insert into the pET-41a (+) vector sequence. The plasmid was virtually cut utilizing the pAD1 sense primer and pAD1 anti primer from the PCR procedure. A restriction digest experiment was designed to confirm the identity of the PCR product. The two restriction endonucleases that cut the PCR product at least once was HgaI and XspI.
...bioanalytical systems which based on electrochemiluminescence detection and evanescent field fluorescent detection showed the best sensitivities (Dupuy et al., 2009). The power of immunoblotting is extended with this method in order to provide a quantitative analysis of differential expression of active and parental proteins (Tibes et al., 2006). Moreover, by using RPPA, samples can be spotted at same time which is suitable for retrospective analysis of large number of specimens. This technique which can be used to analyze large number of proteins from each sample is suitable to analyze the population of cells that present in low numbers. On the other hand, this technique also has limitation which it only identifies to known proteins or targets only (Tibes et al., 2006). However, it stills a useful technique that use in the study of functional proteomics analysis.
... similarities between proteins exhibiting homology, and inspecting the AFP nucleic acid sequence in comparison with proteins showing similarities.
Thavaselvam, Duraipandian, and Rajagopalan Vijayaraghavan. "Abstract." National Center for Biotechnology Information. U.S. National Library of Medicine, 29 Dec. 0005. Web. 04 May 2014.
In the article, “A Simpler Path, Authors Say, is Key to Community-College Completion,” addresses the implementations of the guided pathway’s model, and the benefits and limitations of streamlining the model to community college campuses. This model challenges the traditional “cafeteria style” model of advising, (Mangan, 2017) by introducing a more structured learning-centered approach. Academic advising typically includes helping students develop a clearer understanding of their course of study, and helps develop the skills needed to meet a student’s college and career goals. The guided pathways model provides a way to ensure students stay on track towards the completion of their program, and further job advancement (Bailey et al., 2015).
1. Expression of genome information: I would expect to find the protein helicase in the 41% of the genes that function as expression of genome information. I believe helicase would be present because is a protein needed in order for single strand of DNA to be copied. It uses hydrolysis at the replication fork to unwind the DNA from its double helix structure to make it possible to copy the single strand. This is very important for gene expression.
DNA profiling is used in a variety of ways, such as establishing proof of paternity, or identifying siblings. While DNA contains material common to all humans, some portions are unique to each individual; thus, DNA testing can help solve crimes by comparing the DNA profiles of suspects to offender samples.
Genomics is undergoing rapid development from the analysis, mapping and sequencing of genomes to development about genome function. [Hieter and Boguski, 1997] Genomics looks at the analysis of DNA sequences whilst functional genomics is used to understand the relation of genes and proteins. [Fields et al., 1999] The analysis of genomes has more recently been divided into two groups; functional and structural genomics. Structural genomics is the first phase of genome analysis, which produces an organisms’ genetic, transcript and physical maps. [Hieter and Boguski, 1997] The purpose of structural genomics is the allocation of three-dimensional structures to proteomes; which has given a new viewpoint on protein families and folds, and domain structures within gene sequences. [Teichmann et al., 1999]
Life Science Core at UCLA, Martin, L., Chen, K., Johnson, L., Foley, R., & Murotake, R. (2005). Analysis of Protein Size and Subunit Composition Using SDS- Polyacrylamide Gel Electrophoresis. Los Angeles, CA.
Distinct characteristics are not only an end result of the DNA sequence but also of the cell’s internal system of expression orchestrated by different proteins and RNAs present at a given time. DNA encodes for many possible characteristics, but different types of RNA aided by specialized proteins sometimes with external signals express the needed genes. Control of gene expression is of vital importance for an eukaryote’s survival such as the ability of switching genes on/off in accordance with the changes in the environment (Campbell and Reece, 2008). Of a cell’s entire genome, only 15% will be expressed, and in multicellular organisms the genes active will vary according to their specialization. (Fletcher, Ivor & Winter, 2007).
Jena, Anupam B., Seth Seabury, Darius Lakdawalla, and Amitabh Chandra. "Abstract." National Center for Biotechnology Information. U.S. National Library of Medicine, 18 Aug. 2011. Web. 01 May 2014.
A polypeptide chain is a series of amino acids that are joined by the peptide bonds. Each amino acid in a polypeptide chain is called a residue. It also has polarity because its ends are different. The backbone or main chain is the part of the polypeptide chain that is made up of a regularly repeating part and is rich with the potential for hydrogen-bonding. There is also a variable part, which comprises the distinct side chain. Each residue of the chain has a carbonyl group, which is good hydrogen-bond acceptor, and an NH group, which is a good hydrogen-bond donor. The groups interact with the functional groups of the side chains and each other to stabilize structures. Proteins are polypeptide chains that have 500 to 2,000 amino acid residues. Oligopeptides, or peptides, are made up of small numbers of amino acids. Each protein has a precisely defined, unique amino acid sequence, referred to as its primary structure. The amino acid sequences of proteins are determined by the nucleotide sequences of genes because nucleotides in DNA specify a complimentary sequence in RNA, which specifies the amino acid sequence. Amino acid sequences determine the 3D structures of proteins. An alteration in the amino acid sequence can produce disease and abnormal function. All of the different ways
Polyacrylamide gels are commonly used for protein separation by virtue of being chemically inert , easy staining with silver nitrate and Coomassie blue dye (dyes such as agarose stain completely prevented the identification of species in the electrophoretogram ) , the pores are easyly adjustable through control of acrylamide and bis- acrylamide are polymers that form the gel.
Proteins (macronutrient), which are found in animal products, nuts and beans, they help to build new cells, maintain tissue and synthesis new proteins essential for performing basic bodily functions. Proteins are in abundance in the human body and are present in the outer and inner membranes of all living cells (Dummies, 2018). Proteins are essential for building new cells, maintaining tissue and helping new proteins needed for basic bodily function (