The NCBI QBLAST Package
NCBI provides a standardized API called URLAPI to formulate and dispatch direct HTTP-encoded requests to the NCBI QBlast system. The URLAPI provides a URL and a mechanism to set parameters that allows users to send sequences for BLAST searches. 1. The user provides BLAST parameters through a URL using the HTTP POST method 2. The QBlast service returns a Request Identifier RID and a Request Time of Execution RTOE, measured in seconds for the search, which provide respectively, a unique...
Running Genscan Analyses
Running and interpreting a Genscan analysis is rather straightforward. Point your browser to the Genscan server at MIT http genes.mit.edu GENSCAN.html Fig. 5.2 . For this exercise we will use a 175 kilobase human bacterial artificial chromosome BAC with the accession number AC092818 from NCBI. Genscan has been 'trained' to work with vertebrate, arabidopsis and maize sequences Fig. 5.3 . Since we are analyzing a human BAC, we choose the vertebrate option. We will use the default sub-optimal exon...
Requestldentifier
Fig. 3.4. Structure of the SwingBlast application The Blast class extends the Observable class, which represents an observable object, an instance of which can be observed for any changes that occur to the object. When an observable instance changes that is, when an object that is being observed changes , the notifyobservers method is called and causes the observer to be notified of the change by a call to the observer's update method. In this case, we want to observe the Blast class for...
Performing a BLAST Analysis
Before we can build a BLAST application, we need to understand how BLAST searches are performed using the NCBI BLAST service. BLAST is actually a suite of programs - the particular choice of program s depends on the type of input sequence amino acid or nucleotide and the type of the database to be searched against protein or nucleotide . The most commonly used search programs and their applications are described in Table 2.1. Compares a nucleotide query sequence against a nucleotide sequence...
Implementing JQBIast
We will now build the JQBIast application that allows users to send multiple simultaneously BLAST queries using the classes we described above. To implement the NCBI QBlast package, we just need to extend the Blast class and provide an implementation of the methods as described above. We will call the instance of the Blast class JQBIast as shown below public class JQBIast extends Blast implement Blast methods We will create a file called QBlast. java to implement this code. It is up to the...
Coding the SwingCaBIO Application
SwingCaBio defines the application interface that the user interacts with to send and retrieve queries using the caCORE API. SwingCaBio is based on the same Swing elements and concepts that were described in Chapter 1. SwingCaBio extends JFrame in order to generate a basic container for the application. SwingCaBio also extends DocumentListener to listen to the JTextField objects in order to enable or disable the corresponding buttons that run the report. The constructor swingCaBio calls the...
Analyzing GenScan Output
The GenScan header gives information on the input sequence and the parameters used such as name, size and isochore classification categorization based on GC content of the sequence, and the matrix used for the analysis Humanlso.smat . The body of the analysis consists of the predicted peptide and the corresponding CDS sequences. As is evident from the output there were eight predicted peptides in this sequence. The complete gene structure of each peptide is listed after the header Table 5.1 . '...
X ElHage N et al Synergistic increases in
We could use regular expressions to capture the PMID and other information if all the MEDLINE records had the same standard format. A few of these tags are not present wherever information is not available. For example, sometimes the abstract is not available. In such cases the AB tag is not present in the MEDLINE record which makes it a little more difficult to construct a regular expression that is generic enough for all cases. We demonstrate an alternate method that locates the position of...
Creating the JcaBIO Application
We will create an application based on the caBIO API that we will call JcaBIO to demonstrates how data pertaining to the Gene and the Agent object can be retrieved using caBIO API. We will create three search functions as outlined below that will define the business logic of the application Gene search function The gene search function will create a report that provides information such as gene name and symbol, Unigene Cluster ID, associated GO terms, gene product name and aliases. Pathway...
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Fig. 3.11. Saving BLAST results in a local file Fig. 3.12. Saving BLAST results in a local file Fig. 3.12. Saving BLAST results in a local file Note that if a file of that name already exists, the application warns the user and provides an option to overwrite the existing file or save it with a different name Fig. 3.13 . C U lasttolastn_results.txt already exists. SB Do you want to overwrite To rename the Tile select No, Fig. 3.13. Saving BLAST results in a different file This functionality is...