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Genome Annotation and Multiple Sequence Allignment.



Procedure :


Go to simulator tab to know more about the ASAP.


Step 1: From the tool bar select “comparative genomics”. All throughout the ASAP, one would be working with a specific genome, or a set of experiments on that genome. To begin, select a genome from the drop down menu. Click OK. It redirects to a page where one has to select a sequence version or an experiment set. Different versions of query related to the genome are critical. The home page is shown below.


Figure1: Selecting Gene and version



Select the corresponding option from the different sequence options given below. Select the features from “features type” in the annotation page, indicating the genome of the related feature, the gene name, type of relationship, and the curated approval status.


 Figure2: Setting up parameters.



By clicking on the show orthologs it will redirects to the gene expression result data based on the feature ID, feature type, product of the genes. Feature ID provides the whole information of the gene being added in ASAP until the current time. Download DB-Friendly Format will allow one to retreive the data as such in text file. By clicking on the “next” and “previous” button will redirects to their consequetive pages of the feature list.The screen shot is shown below.


 Figure3: Result page of Show orthologs.



Each record in the feature list has full information of the entire annotated gene. By clicking on the list it will redirects to the information related page.


 Figure4 : Result of each gene list




BLAST procedure:


In ASAP, BLAST searches for identifying putative gene functions.


Select the type of query sequence, enter the query sequence of DNA/protein sequence in FASTA format in the given query box or upload a file which contains the FASTA sequence and set up the parameters like search type, Database sequence type, E-value, filter , description and alignment. Choose an appropriate database according to the query provided. Select the genome and version from the database which is related to the query sequence as shown below.


Figure5:ASAP BLAST home page.



To run the BLAST search, one can give the sequence and set the parameters related to the query sequence.


 Figure 6: Settiing up parameters



After giving the input and setting up the parameters click on search, it will redirects to the BLAST result page. It shows the information like reference regarding ASAP BLAST program and reference for composition based statistics. It shows full information like number of words in query sequence, GI, Accession number, protein name and the databases are selected by the user. List of the sequences, number of sequences in database, number of letters in database, lambda value and gapped lamda value are the other information one can obtain. Matrix gives the information about the gap penalities, sequences, hits, extensions and databases.


 Figure 7: BLAST result page.









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