Basic Protein Sequence Analysis
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- Abstract
- Table of Contents
- Materials
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- Literature Cited
Abstract
Prediction of molecular function of proteins has become an important task in the genomics era. A wide variety of sequence analysis tools are available to biologists for this task. We have selected one or two primary protocols for tasks such as domain detection, subcellular localization, and motif detection. We also present a strategy for integration of results from different protocols. All the resources needed for these protocols are accessible via publicly available Web servers and databases and require little or no computational expertise.
Keywords: protein sequence analysis; domain detection; subcellular localization; motif detection
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PDF or HTML at Wiley Online LibraryTable of Contents
- Basic Protocol 1: Identifying Structural and Functional Domains Using Integrated Meta‐Servers
- Support Protocol 1: Guidelines for Understanding Results of Analyses from Integrated Meta‐Servers
- Alternate Protocol 1: Identifying Structural and Functional Domains Using the NCBI CD‐Search
- Support Protocol 2: Guidelines for Understanding Results of Analyses from the NCBI CD‐Search
- Alternate Protocol 2: Predicting Structural Domains and Secondary Structure Using 3D‐PSSM
- Support Protocol 3: Guidelines for Understanding Results of Analyses from the 3D‐PSSM Server
- Basic Protocol 2: Predicting Helical Transmembrane Regions and Subcellular Localization
- Support Protocol 4: Guidelines for Understanding Results of Predictions of Helical Transmembrane Regions and Subcellular Localization
- Alternate Protocol 3: Predicting the Subcellular Localization of a Protein Using Targetp
- Support Protocol 5: Guidelines for Understanding Results Predicting the Subcellular Localization of a Protein Using TargetP
- Basic Protocol 3: Predicting Key Functional Residues and Motifs using the Prosite Web Server
- Support Protocol 6: Guidelines for Understanding Results of Searches Done Using the Prosite Web Server
- Support Protocol 7: Homolog Identification
- Commentary
- Literature Cited
- Figures
- Tables
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PDF or HTML at Wiley Online LibraryMaterials
Basic Protocol 1: Identifying Structural and Functional Domains Using Integrated Meta‐Servers
Materials
Support Protocol 1: Guidelines for Understanding Results of Analyses from Integrated Meta‐Servers
Materials
Alternate Protocol 1: Identifying Structural and Functional Domains Using the NCBI CD‐Search
Materials
Support Protocol 2: Guidelines for Understanding Results of Analyses from the NCBI CD‐Search
Materials
Alternate Protocol 2: Predicting Structural Domains and Secondary Structure Using 3D‐PSSM
Materials
Support Protocol 3: Guidelines for Understanding Results of Analyses from the 3D‐PSSM Server
Materials
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PDF or HTML at Wiley Online LibraryFigures
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Figure 2.11.1 FASTA format of AVR2_HUMAN protein sequence. The Swiss‐Prot accession number is P27037 and the Swiss‐Prot ID is AVR2_HUMAN. View Image -
Figure 2.11.2 SMART sequence submission form. (A ) Submission of sequence in FASTA format. (B ) Submission using the Swiss‐Prot accession number in the box marked with arrow. View Image -
Figure 2.11.3 Sequence submission options in SMART. View Image -
Figure 2.11.4 SMART results for AVR2_HUMAN. Integrated results from several servers show an N‐terminal signal peptide, two PFAM domains, a transmembrane domain, and a low‐complexity region. View Image -
Figure 2.11.5 CD‐Search sequence submission form. View Image -
Figure 2.11.6 Results from CD‐Search. (A ) The output gives a graphic display and E‐values of hits. (B ) Pairwise alignment of the query with the top hit. View Image -
Figure 2.11.7 Multiple sequence alignment of AVR2_HUMAN kinase domain with a conserved kinase domain hit. The columns marked with # have been identified as critical for kinase function. View Image -
Figure 2.11.8 Submission form and results page from 3D‐PSSM server. (A ) The submission form; (B ) the results page. View Image -
Figure 2.11.9 Sequence alignments produced by 3D‐PSSM (A ) Alignment of query to its homologs. (B ) Pairwise alignment and comparison of secondary structure and solvent accessibility predictions for the query with that of the hit (structural domain). View Image -
Figure 2.11.10 TMHMM ouput for AVR2_HUMAN. Shown are results in the “extensive with graphics” format. A summary of results is followed by a graphic display. The x axis on the graph represents amino acid positions in the query sequence and the y axis represents the probability of a residue to be in a TM. The peaks indicate positions with higher probability of being a TM domain. The predictions of TM and topology are indicated above a y axis value of 1. The region predicted to be inside (cytoplasmic) is represented with a blue line (marked as INSIDE in this figure) and the region on the outside (extracellular) is represented in pink (labeled OUTSIDE in this figure). View Image -
Figure 2.11.11 TargetP prediction of the subcellular localization of AVR2_HUMAN. View Image -
Figure 2.11.12 Prediction of patterns by PROSITE for AVR2_HUMAN. (A ) results of profile search; (B ) results of pattern search. View Image
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Literature Cited
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