(Expasy)

This slides gives you a knowledge about some categories & and how we use different databases and tool and how they work for what function.

1. expasy Expert protein analysis system

2. introduction The ExPASy (the Expert Protein Analysis System) World Wide Web server which is provided as a service to the life science community. It provides access to a variety of databases and analytical tools dedicated to proteins and proteomics. ExPASy databases include SWISS-PROT , TrEMBL , SWISS-2DPAGE, PROSITE, ENZYME and the SWISS-MODEL repository.

3. Continue Analysis tools are available for specific tasks relevant to proteomics, similarity searches, pattern and profile searches, post-translational modification prediction, topology prediction, primary, secondary and tertiary structure analysis and sequence alignment.

4. history ExPASy was created in August 1993: it was one of the first Web servers for biological sciences. Since that date it has undergone constant modifications and improvements In June 2011 the SIB ExPASy Bioinformatics Resources Portal was launched by the SIB Swiss Institute of Bioinformatics. ExPASy has been designed, developed and maintained by the SIB Web Team in co-operation with several other SIB groups and ExPASy users.

5. Home page of expasy

6. Visual guidance interface:

7. Home page of uniport database

8. Sequence of insulin-like growth factor 1 receptor

9. Transcription and translation tool

10. Transcription and translation tool In this tool we input a dna sequence . Transcribe messenger RNA (mRNA) is a temporary copy of the gene sequence in which protein is encoded. Translated into protein sequence (amino acid) Can be reverse transcribed Dna sequence

11. How the tool is work

12. THANKS

13. Genomics By: Hamza Qureshi

14. This category contains tools and databases related to genes , sequences ,similarity, alignment and characterisation. Further divided into 3 sub categories: Sequence alignment Similarity search Characterization /annotation

15. 1 . Sequence alignment Tools Contains various tools for Multiple sequence alignments , locally and globally. Some are supported by expasy (SIB) while others are from external resources.

16. ClustalW ( Multiple alignment of nucleic acid and protein sequences ) Clustal  W is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. It calculates the best match for the selected sequences, and lines them up so that the identities, similarities and differences can be seen.

17. Result of alignment open in WordPad

18. Similarity search These tools  search sequence  databases by using alignment to a query  sequence . By statistically assessing how well database and query  sequences  match one can infer homology and transfer information to the query  sequence .

19. LALIGN Tool for pairwise alignment This tool finds multiple matching subsegments in two sequences, locally or globally from the FASTA package.

20. Results

21. Characterisation/Annotation DATABASES and Tools This category contains databases and tools for detection of variation as a result of differences in either DNA sequences or specific  genes  or modifying factors. ... In contrast,  genetic characterization  refers to the description of attributes that follow a Mendelian inheritance or that involve specific DNA sequences.

22. OMA Web based database interface for orthology prediction OMA is a project that aims to identify orthologs among publicly available, complete genomes. With many hundreds of genomes analyzed to date, OMA is one of the largest projects of its kind. The OMA (“Orthologous MAtrix ”) project is a method and database for the inference of orthologs among complete genomes. The distinctive features of OMA are its broad scope and size,  high quality of inferences , feature-rich web interface,  availability of data in a wide range of formats and interfaces , and frequent update schedule of two releases per year.

23. Typical uses The OMA project provides different types of ortholog representations and tools, each useful for different contexts and applications.  Identify orthologous marker genes to infer a species tree Identify all orthologs of a gene in a given set of organisms Identify all genes in tetrapodes that descended from the ancestral β- hemoglobin Assess the conservation of local genomic neighbourhood across multiple species Apply the OMA pipeline to custom genome/transcriptome data Consult inferred Gene Ontology terms for a particular gene present in OMA. Propagate functional annotations between two specific genomes Align two whole genomes Align protein–protein interaction networks between two genomes

24. List of related results with mentioned species. Select the desired result.

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