Structure Similarity Based Search Engines: Combinatorial Extension, VAST and DALI | Proteomics Tools: ExPASy Server and EMBOSS

Quick Overview: Structure similarity search compares the three-dimensional structures of proteins to identify structurally related proteins. Important structure comparison approaches include Combinatorial Extension (CE), VAST and DALI. For proteomics and protein sequence analysis, important resources include the ExPASy server and EMBOSS.

In bioinformatics, biological information can be studied at several levels. We can compare DNA sequences, RNA sequences, protein sequences and three-dimensional protein structures. Sequence comparison is extremely useful, but sometimes two proteins may have very different sequences while still having similar three-dimensional structures.

This is why protein structure similarity searching is important. A protein's three-dimensional structure can remain evolutionarily conserved even when its amino acid sequence has changed considerably. By comparing structures, researchers can discover relationships that may not be obvious from sequence comparison alone.

Three important structure similarity approaches frequently discussed in bioinformatics are:

Combinatorial Extension (CE)
VAST – Vector Alignment Search Tool
DALI

The second part of this topic focuses on proteomics tools. Proteomics deals with the large-scale study of proteins, including their identification, properties, functions, interactions and expression. Two important bioinformatics resources commonly studied in this context are:

ExPASy Server
EMBOSS

Exam Tip: Remember the broad distinction: CE, VAST and DALI → protein structure comparison; ExPASy and EMBOSS → protein/sequence analysis and bioinformatics tools.

1. Introduction to Structure Similarity Searching

A protein is not just a sequence of amino acids. The amino acid sequence folds into a particular three-dimensional structure, and that structure is closely related to the protein's function.

Two proteins can sometimes have low sequence similarity but still adopt similar three-dimensional structures. This may happen because evolutionary changes can modify the amino acid sequence while preserving the overall structural arrangement required for function.

Structure similarity searching therefore asks a different question from sequence similarity searching:

Sequence search: Which proteins have similar amino acid sequences?

Structure search: Which proteins have similar three-dimensional structures?

Structure comparison is especially useful for studying protein evolution, structural classification, remote relationships and possible functional relationships.

2. Why Compare Protein Structures?

Protein structure comparison is useful because structure can sometimes reveal evolutionary relationships that are difficult to detect from sequence alone.

Major reasons for structural comparison

Identify structurally related proteins.
Investigate evolutionary relationships.
Identify possible homologous proteins.
Find proteins with similar folds.
Support protein function prediction.
Study structural domains.
Compare experimentally determined structures.
Investigate remote structural relationships.
Support structural classification.
Assist drug discovery and structural biology.

For example, suppose an unknown protein has a sequence that is highly divergent from known proteins. A sequence search might produce weak results. A structure comparison could nevertheless identify a similar fold and provide an important clue about its evolutionary or functional relationship.

3. Sequence Similarity vs Structure Similarity

Feature	Sequence Similarity	Structure Similarity
Compared object	DNA, RNA or protein sequence	3D protein structure
Main information	Order of residues	Spatial arrangement of atoms/residues
Examples	BLAST, FASTA	CE, VAST, DALI
Useful for	Sequence homology and annotation	Structural relationships and fold comparison
Input	Sequence	Usually experimentally determined or modeled structure

Important concept: Similar structure can sometimes be detected even when sequence similarity is weak.

4. Combinatorial Extension (CE)

Combinatorial Extension (CE) is a protein structure comparison method developed to identify structural similarities between proteins.

The basic idea is to represent protein structures using short structural fragments and then identify combinations of aligned fragment pairs that produce a good structural alignment.

Instead of trying every possible complete structural alignment directly, CE uses a systematic approach based on aligned fragment pairs (AFPs) and extends promising structural matches.

What does "Combinatorial Extension" mean?

The name describes the basic idea of the method. Structural matches are first identified as small compatible pieces and then extended to form longer structural alignments.

Simple concept:
Protein structure
↓
Identify compatible structural fragments
↓
Build aligned fragment pairs
↓
Extend promising combinations
↓
Obtain structural alignment
↓
Calculate structural similarity

5. Working Principle of CE

A simplified explanation of the CE approach is as follows:

Take two protein structures for comparison.
Divide or represent the structures using short structural fragments.
Identify possible corresponding fragment pairs.
Evaluate whether neighboring fragment pairs are structurally compatible.
Extend compatible fragment pairs into longer alignments.
Calculate structural similarity and alignment statistics.
Report the resulting structural alignment.

The actual implementation involves geometric and computational calculations, but the basic idea can be remembered as:

CE = Find small compatible structural pieces → extend them → obtain structural alignment.

Importance of CE

Protein structure comparison
Structural alignment
Fold comparison
Protein classification
Evolutionary studies
Remote structural relationship analysis

6. How CE-Based Structure Searching Works

A typical CE-based analysis starts with a known protein structure. The structure is compared with other structures in an appropriate structural database or structure-comparison environment.

Step 1: Obtain a protein structure, usually from a structural database such as the Protein Data Bank.

Step 2: Provide the structure identifier or structural coordinates to the appropriate CE implementation.

Step 3: Compare the query structure against candidate structures.

Step 4: Examine the structural alignment.

Step 5: Examine RMSD, alignment length and other structural statistics where provided.

Step 6: Investigate the biological annotation of the structurally similar proteins.

A CE result should therefore not be interpreted using a single number. Structural coverage, RMSD, alignment length and biological context should all be considered.

7. VAST

VAST stands for Vector Alignment Search Tool.

VAST is an NCBI structure comparison system designed to identify structurally similar proteins. It compares protein structures by representing local structural features using vectors and searching for similar structural arrangements.

The NCBI structure resources have used VAST to compare protein structures and identify related structures.

Basic idea of VAST

A protein's three-dimensional structure can be described in terms of the spatial relationships between secondary-structure elements such as alpha helices and beta strands. VAST uses these structural relationships to find similar structures.

VAST in simple language:
Protein structure → Represent structural relationships → Compare vectors/structural elements → Find similar structures

8. Working Principle of VAST

A simplified VAST workflow can be understood as follows:

Start with a protein structure.
Identify secondary-structure elements.
Represent their spatial relationships using vectors.
Compare structural relationships between proteins.
Identify compatible structural arrangements.
Generate structural alignments.
Rank structurally similar proteins.

VAST is particularly useful when researchers want to search structural databases for proteins that have similar three-dimensional arrangements.

What can VAST tell us?

A structure comparison may help reveal:

Similar protein folds
Structurally related proteins
Conserved structural domains
Potential evolutionary relationships
Structural relationships between proteins from different organisms

9. How to Use VAST

The exact NCBI interface can change over time, but the general workflow for using structure-comparison resources is straightforward.

Step 1: Open the NCBI Structure resources.

Step 2: Search for the protein structure using its PDB identifier, protein name or another appropriate identifier.

Step 3: Open the structure record.

Step 4: Locate the structure comparison or related-structure information.

Step 5: Examine structures identified as similar.

Step 6: Open individual structural alignments.

Step 7: Compare alignment length, RMSD and other available similarity information.

Step 8: Examine the biological functions of the matching proteins.

Practical Tip: VAST is strongly associated with NCBI structure resources. If an older textbook or syllabus specifically mentions VAST, remember its full form: Vector Alignment Search Tool.

10. DALI

DALI is a well-known protein structure comparison method and server developed for finding structurally similar proteins.

The name is commonly associated with Distance-matrix ALIgnment.

The central idea of DALI is to represent a protein structure using a distance matrix describing distances between residues and then compare structural distance patterns between proteins.

DALI basic concept:
3D Protein Structure
↓
Calculate inter-residue distance relationships
↓
Construct structural distance representation
↓
Compare distance patterns
↓
Find structurally similar proteins

11. Working Principle of DALI

DALI uses the internal geometry of a protein rather than relying only on amino acid sequence.

The basic concept can be explained using a simple example.

Imagine two proteins. Their amino acid sequences may be quite different, but the distances between corresponding structural elements may be similar. If these spatial relationships are preserved, a structure-comparison method can identify the relationship.

Simplified DALI workflow

Obtain the three-dimensional protein structure.
Represent the structure through inter-residue distance information.
Compare distance patterns with structures in the database.
Identify compatible structural arrangements.
Calculate structural similarity scores.
Generate structural alignments.
Rank significant structural matches.

DALI Z-score

One important concept associated with DALI is the Z-score. It is used to indicate how significant a structural similarity is relative to the background distribution used by the method.

In general, a higher DALI Z-score indicates stronger structural similarity, although the precise interpretation should be made in the context of the DALI results and the structures being compared.

Exam Tip: DALI → Distance-matrix alignment. Remember the connection between DALI and distance matrices.

12. How to Use DALI

The DALI server is particularly useful for structural comparison. A general workflow is:

Step 1: Open the official DALI server.

Step 2: Select the appropriate structure-search option.

Step 3: Provide a PDB identifier or an appropriate protein structure input according to the current interface.

Step 4: Submit the search.

Step 5: Allow DALI to compare the query structure with available structures.

Step 6: Examine the ranked list of structural matches.

Step 7: Check the DALI Z-score, RMSD, alignment length and sequence identity where available.

Step 8: Open promising structural matches and inspect their alignments.

Step 9: Investigate the biological function and evolutionary context of the matching proteins.

13. CE vs VAST vs DALI

Feature	CE	VAST	DALI
Full name	Combinatorial Extension	Vector Alignment Search Tool	Distance-matrix alignment
Main focus	Structural alignment using fragment pairs and extension	Structural comparison using vector representations	Structural comparison using distance relationships
Input	Protein structures	Protein structures	Protein structures
Main output	Structural alignment and similarity statistics	Structurally related proteins and alignments	Structural matches, alignments and Z-scores
Important concept	Aligned fragment pairs	Vectors representing structural relationships	Distance matrix
Major use	Structure alignment/search	Structure search	Structure similarity search

Easy Memory Trick:
CE → Extend structural fragments
VAST → Vector Alignment
DALI → Distance-matrix alignment

14. Structure Similarity Search Workflow

The following SVG summarizes how a protein structure can be analyzed using CE, VAST and DALI.

15. What is Proteomics?

Proteomics is the large-scale study of the complete set of proteins produced by a cell, tissue or organism under a particular biological condition. This complete protein complement is commonly referred to as the proteome.

Proteomics can investigate:

Protein identification
Protein abundance
Protein expression
Protein modifications
Protein-protein interactions
Protein structure
Protein localization
Protein function
Protein pathways

Bioinformatics plays a major role in proteomics because large-scale protein experiments generate large datasets that need computational analysis.

16. ExPASy Server

ExPASy stands for Expert Protein Analysis System. It is a bioinformatics resource portal operated by the Swiss Institute of Bioinformatics (SIB).

ExPASy provides access to a wide range of protein and proteomics-related databases and analysis tools. It is particularly useful for protein sequence analysis, protein identification, molecular properties and functional investigation.

The ExPASy ecosystem includes resources and tools for areas such as protein sequence analysis, proteomics, structural biology and molecular biology.

ExPASy in simple language:
It is a major bioinformatics portal where researchers can access different tools and databases for analyzing proteins and other biological information.

Why is ExPASy important?

Protein sequence analysis
Protein identification
Calculation of molecular properties
Protein database access
Proteomics analysis
Enzyme and protein information
Access to SIB bioinformatics resources

17. Important ExPASy Tools

Tool/Resource	Main Use
ProtParam	Calculate theoretical physicochemical properties of a protein sequence.
ProtScale	Analyze amino acid sequence properties along the sequence.
Compute pI/Mw	Calculate theoretical isoelectric point and molecular weight.
Swiss-Prot / UniProt resources	Access curated protein sequence and functional information.
PeptideMass	Calculate theoretical peptide masses generated by proteolytic digestion.
ScanProsite	Search protein sequences for PROSITE signatures.

Important: ExPASy is best understood as a bioinformatics resource portal, rather than a single analysis program.

18. How to Use ExPASy Step by Step

Here is a simple workflow for beginners.

Step 1: Open the official ExPASy website.

Step 2: Explore the available protein and proteomics tools.

Step 3: Select the tool appropriate for your research question.

Step 4: For sequence-based tools, paste the amino acid sequence in the input field.

Step 5: Submit the analysis.

Step 6: Examine the output carefully.

Step 7: Record relevant parameters and predictions.

Step 8: Confirm important findings using independent databases or tools.

Example: Using ProtParam

Suppose you have a protein sequence and want to estimate its molecular weight and isoelectric point.

1. Open ExPASy.

2. Open the ProtParam tool.

3. Paste your protein sequence.

4. Submit the sequence.

5. Examine the calculated molecular weight.

6. Examine the theoretical pI.

7. Review additional physicochemical properties.

8. Use the information for experimental planning or protein characterization.

19. EMBOSS

EMBOSS stands for European Molecular Biology Open Software Suite.

EMBOSS is an open-source software suite containing a large collection of tools for molecular biology and sequence analysis. It provides programs for sequence manipulation, alignment, analysis, database searching, primer-related tasks and other bioinformatics operations.

Unlike a single-purpose tool, EMBOSS is a large collection of command-line and related bioinformatics applications.

EMBOSS in simple language:
EMBOSS is a toolbox containing many different programs for analyzing DNA, RNA and protein sequences.

Why is EMBOSS important?

Sequence analysis
Pairwise sequence alignment
Multiple sequence analysis
Sequence format conversion
Restriction site analysis
Primer analysis
Protein property analysis
Motif and pattern analysis
Sequence statistics
Database searching

20. Important EMBOSS Programs

EMBOSS Program	Main Function
needle	Global pairwise sequence alignment.
water	Local pairwise sequence alignment.
getorf	Identify possible open reading frames in nucleotide sequences.
transeq	Translate nucleotide sequences into amino acid sequences.
sixpack	Display translations in six reading frames.
pepstats	Calculate statistics for protein sequences.
infoseq	Display information about sequences.
seqret	Read and convert sequence formats.
restrict	Identify restriction enzyme recognition sites.
cons	Generate consensus sequences from aligned sequences.

Important EMBOSS Programs for Exams

needle → Global alignment
water → Local alignment
getorf → ORF identification
transeq → Sequence translation
pepstats → Protein sequence statistics
seqret → Sequence format conversion

21. How to Use EMBOSS

EMBOSS can be used through command-line programs and through web interfaces that provide access to EMBOSS applications.

Example 1: Global Alignment Using needle

Step 1: Obtain two protein or nucleotide sequences.

Step 2: Open an EMBOSS environment containing the needle program.

Step 3: Provide the first sequence.

Step 4: Provide the second sequence.

Step 5: Select suitable scoring parameters if required.

Step 6: Run the program.

Step 7: Examine the global alignment.

Example 2: Local Alignment Using water

Step 1: Open the EMBOSS water program.

Step 2: Enter the two sequences.

Step 3: Submit the analysis.

Step 4: Examine the best local matching region.

Example 3: Translation Using transeq

Step 1: Enter a nucleotide sequence.

Step 2: Open the transeq program.

Step 3: Select the appropriate translation settings.

Step 4: Run the analysis.

Step 5: Examine the resulting amino acid sequence.

22. ExPASy vs EMBOSS

Feature	ExPASy	EMBOSS
Type	Bioinformatics resource portal	Open-source software suite
Organization/association	Swiss Institute of Bioinformatics	European Molecular Biology Open Software Suite
Main focus	Protein and proteomics resources and tools	Broad molecular sequence analysis
Protein analysis	Strong focus	Many protein analysis programs
DNA/RNA analysis	Available through resources/tools	Extensive sequence analysis capabilities
Examples	ProtParam, ProtScale, ScanProsite	needle, water, getorf, transeq, pepstats
Typical use	Protein characterization and access to bioinformatics resources	Sequence manipulation and computational analysis

Memory Trick:
ExPASy = Protein analysis portal
EMBOSS = Molecular biology software toolbox

23. Integrated Bioinformatics Workflow

In real research, these tools are often used as complementary resources rather than independently.

24. Applications

A. Applications of CE, VAST and DALI

Protein structure comparison
Structural classification
Fold identification
Evolutionary analysis
Remote homology investigation
Protein function prediction
Structural domain analysis
Comparative structural biology
Drug discovery and target analysis

B. Applications of ExPASy

Protein physicochemical characterization
Protein sequence analysis
Proteomics data interpretation
Protein identification
Motif analysis
Enzyme and protein information retrieval

C. Applications of EMBOSS

DNA and protein sequence analysis
Global and local alignment
ORF identification
Sequence translation
Sequence format conversion
Protein statistics
Restriction site analysis
Consensus sequence generation
Primer and sequence analysis

25. Advantages

Resource	Major Advantages
CE	Useful for structural alignment and identification of structurally compatible regions.
VAST	Useful for searching and comparing protein structures in NCBI structural resources.
DALI	Powerful structure comparison based on spatial distance relationships.
ExPASy	Large ecosystem of protein and proteomics resources and analysis tools.
EMBOSS	Large collection of open-source molecular biology sequence-analysis programs.

26. Limitations

Structural Search Limitations

Results depend on the quality of the input structure.
Different structural comparison algorithms can produce different alignments.
Structural similarity does not automatically prove identical biological function.
Large proteins and multi-domain proteins can be difficult to interpret.
Alignment coverage is important when evaluating a structural match.

ExPASy Limitations

It is a portal containing many resources, so beginners may initially find it difficult to choose the correct tool.
Individual tools have their own assumptions and limitations.
Predicted physicochemical properties are theoretical and should not be treated as experimental measurements.

EMBOSS Limitations

Many programs are command-line based and may require practice.
Users need to understand sequence-analysis parameters.
Different programs answer different biological questions.
Computational results still require biological interpretation.

Important: A structural match or sequence-analysis result is evidence that needs biological interpretation. Never assign protein function based on a single computational result without checking additional evidence.

27. Important Exam Facts

1. CE stands for Combinatorial Extension.

2. CE is a protein structure comparison/alignment method.

3. CE uses aligned fragment pairs and extends compatible structural matches.

4. VAST stands for Vector Alignment Search Tool.

5. VAST is associated with NCBI structure comparison.

6. VAST uses structural representations based on spatial relationships of structural elements.

7. DALI is associated with distance-matrix alignment.

8. DALI compares protein structures using distance relationships within the structures.

9. DALI results commonly include a Z-score used in assessing structural similarity.

10. ExPASy stands for Expert Protein Analysis System.

11. ExPASy is associated with the Swiss Institute of Bioinformatics.

12. ProtParam is used to calculate theoretical physicochemical properties of proteins.

13. EMBOSS stands for European Molecular Biology Open Software Suite.

14. EMBOSS is an open-source collection of molecular biology software tools.

15. needle performs global pairwise alignment.

16. water performs local pairwise alignment.

17. getorf identifies possible open reading frames.

18. transeq translates nucleotide sequences into protein sequences.

19. pepstats provides protein sequence statistics.

20. Structural similarity and sequence similarity are not the same thing.

28. MCQs

MCQ 1

CE stands for:

A. Computational Extension
B. Combinatorial Extension
C. Comparative Enzyme
D. Cellular Extension

Answer: B. Combinatorial Extension

MCQ 2

Which tool stands for Vector Alignment Search Tool?

A. VAST
B. DALI
C. CE
D. EMBOSS

Answer: A. VAST

MCQ 3

DALI is mainly associated with:

A. Distance-matrix based structure comparison
B. DNA sequencing
C. Gene expression
D. Chemical structure search

Answer: A. Distance-matrix based structure comparison

MCQ 4

Which of the following is a structure similarity search method?

A. BLAST
B. CE
C. GEO
D. PubChem

Answer: B. CE

MCQ 5

ExPASy stands for:

A. Expert Protein Analysis System
B. Experimental Protein Analysis System
C. Expert Peptide Analysis System
D. Enzyme Protein Analysis System

Answer: A. Expert Protein Analysis System

MCQ 6

ProtParam is used for:

A. Protein physicochemical property calculation
B. Protein crystallization
C. DNA sequencing
D. Genome assembly

Answer: A. Protein physicochemical property calculation

MCQ 7

EMBOSS stands for:

A. European Molecular Biology Open Software Suite
B. European Molecular Biological Online Sequence System
C. Experimental Molecular Biology Open Search System
D. European Microbiology Bioinformatics Open Software System

Answer: A. European Molecular Biology Open Software Suite

MCQ 8

Which EMBOSS program performs global pairwise alignment?

A. water
B. needle
C. getorf
D. transeq

Answer: B. needle

MCQ 9

Which EMBOSS program performs local pairwise alignment?

A. needle
B. water
C. pepstats
D. seqret

Answer: B. water

MCQ 10

Which EMBOSS program is used for nucleotide-to-protein translation?

A. transeq
B. needle
C. water
D. restrict

Answer: A. transeq

MCQ 11

Which EMBOSS program is associated with ORF identification?

A. getorf
B. water
C. pepstats
D. seqret

Answer: A. getorf

MCQ 12

Which statement is correct?

A. Structural similarity always means identical function
B. Structural similarity can provide evidence for evolutionary or functional relationships
C. Structure and sequence are exactly the same information
D. DALI is a gene-expression database

Answer: B. Structural similarity can provide evidence for evolutionary or functional relationships

29. Frequently Asked Questions

Q1. What is structure similarity searching?

It is the computational comparison of protein three-dimensional structures to identify structurally related proteins.

Q2. What is CE?

CE, or Combinatorial Extension, is a protein structure comparison method that uses compatible structural fragment pairs and extends them into structural alignments.

Q3. What is VAST?

VAST stands for Vector Alignment Search Tool and is associated with NCBI protein structure comparison.

Q4. What is DALI?

DALI is a protein structure comparison approach based on distance relationships within protein structures.

Q5. What is the main difference between DALI and BLAST?

BLAST primarily compares biological sequences, whereas DALI compares protein structures.

Q6. What is ExPASy?

ExPASy is a major Swiss Institute of Bioinformatics resource portal providing access to protein and proteomics databases and analysis tools.

Q7. What is ProtParam?

ProtParam is an ExPASy tool used to calculate theoretical physicochemical properties of a protein sequence.

Q8. What is EMBOSS?

EMBOSS is an open-source molecular biology software suite containing many sequence-analysis programs.

Q9. What is the difference between needle and water?

In EMBOSS, needle is used for global pairwise alignment, whereas water is used for local pairwise alignment.

Q10. Which tool can translate nucleotide sequence into protein sequence?

The EMBOSS program transeq is used for nucleotide-to-protein translation.

Q11. Which tool is used to identify ORFs in EMBOSS?

The EMBOSS program getorf is used to identify possible open reading frames.

Q12. Can structural similarity prove that two proteins have exactly the same function?

No. Structural similarity can provide strong evidence of a relationship, but biological function should be evaluated using multiple lines of evidence.

30. Last-Minute Revision

Structure Similarity Search
CE → Combinatorial Extension
VAST → Vector Alignment Search Tool
DALI → Distance-matrix alignment

CE
Structural fragments → aligned fragment pairs → extension → structural alignment

VAST
Structural elements → vector representation → structural comparison

DALI
Protein structure → distance relationships → distance-matrix comparison → structural matches

ExPASy
Expert Protein Analysis System → protein/proteomics resource portal

ProtParam
Protein physicochemical properties

EMBOSS
European Molecular Biology Open Software Suite

needle
Global pairwise alignment

water
Local pairwise alignment

getorf
ORF identification

transeq
Nucleotide → Protein translation

pepstats
Protein sequence statistics

31. Important Official Links

Resource	Official Website	Main Use
NCBI Structure	NCBI Structure	Protein structure information and structural resources
VAST	NCBI VAST	Protein structure comparison
DALI	DALI Server	Protein structure similarity searching
ExPASy	ExPASy	Protein and proteomics bioinformatics resources
ExPASy ProtParam	ProtParam	Protein physicochemical properties
EMBOSS	EMBOSS	Sequence analysis tools
Protein Data Bank	RCSB PDB	3D biological macromolecular structures

32. Conclusion

Structure similarity searching is an important part of structural bioinformatics because protein structure can sometimes reveal relationships that are difficult to detect using sequence comparison alone.

Combinatorial Extension (CE), VAST and DALI are important structure comparison approaches. CE uses structural fragment pairs and extension, VAST uses vector-based representations of structural relationships, and DALI is based on distance relationships within protein structures.

The second part of this topic focuses on proteomics and protein-analysis tools. ExPASy provides a large collection of protein and proteomics resources, while EMBOSS provides a broad collection of open-source molecular biology and sequence-analysis programs.

For practical bioinformatics work, these tools are most powerful when used together. A researcher may begin with a protein sequence, calculate its physicochemical properties using ExPASy, analyze or manipulate the sequence using EMBOSS, and then investigate structural relationships using CE, VAST or DALI.

One-Line Revision:
CE = Combinatorial Extension | VAST = Vector Alignment Search Tool | DALI = Distance-matrix alignment | ExPASy = Protein analysis resource portal | EMBOSS = Molecular biology software suite

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Tuesday, 8 September 2026

Structure Similarity Search Engines: Combinatorial Extension, VAST and DALI | Proteomics Tools ExPASy and EMBOSS