Methods in Protein Sequence Analysis


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4.1. Identification of Genes in a Genomic DNA Sequence

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Introduction

This unit is presented as a guide to addressing the issue of what to do with a protein sequence once it is obtained. A theoretical background for protein sequence analysis is provided first, followed by a discussion of matrix methods for sequence comparison 3. Other aspects of protein sequence analysis covered here are alignment methods, scoring matrices, multiple alignments, cluster methods and trees, and identification of functional sites. Volume 00 , Issue 1. If you do not receive an email within 10 minutes, your email address may not be registered, and you may need to create a new Wiley Online Library account.

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Pitfalls of protein sequence analysis

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Computer Methods for Macromolecular Sequence Analysis, Volume 266

Abstract This unit is presented as a guide to addressing the issue of what to do with a protein sequence once it is obtained. Bridge Theoretical Oncogenomics M. Baudis Vital-IT M. Showing 18 records out of 18 total. Categories: proteomics, protein sequences and identification , proteomics experiment - Software type s : website - tool. Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques.


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  • Categories: proteomics, function analysis - Software type s : website - tool. GPMAW lite.

    Introduction

    GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest. Categories: proteomics, protein sequences and identification , function analysis - Software type s : website - database.

    This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20' protein-coding genes found in the human genome. The content of neXtProt is continuously extended so as to provide many more carefully selected data sets and analysis tools. One to Three [Bioinformatics. One to Three converts single letter translations to three letter translations. PepDraw is a tool to draw peptide primary structure and calculate theoretical properties.

    The PoPS project is a set of computational tools for investigating protease specificity. The main PoPS program allows users to model and profile protease specificity and predict substrate cleavage. Other tools are available to search for substrates within proteomes protein databases for organisms , and create simple matrix models of specificity from experimental data. Protein Colourer [EBI]. Protein Colourer is a tool for colouring amino acid sequences.

    Methods in Protein Sequence Analysis

    The default settings will colour the sequence by the hydrophobicity of the amino acids. You can set the colouring scheme by changing the lists associated with each colour. Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI isoelectric point , amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity GRAVY.

    The SwissTree project aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. SwissTree is used for benchmarking at the Orthology Benchmarking web service.

    Methods in Protein Sequence Analysis Methods in Protein Sequence Analysis
    Methods in Protein Sequence Analysis Methods in Protein Sequence Analysis
    Methods in Protein Sequence Analysis Methods in Protein Sequence Analysis
    Methods in Protein Sequence Analysis Methods in Protein Sequence Analysis
    Methods in Protein Sequence Analysis Methods in Protein Sequence Analysis
    Methods in Protein Sequence Analysis Methods in Protein Sequence Analysis
    Methods in Protein Sequence Analysis Methods in Protein Sequence Analysis

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