BIPASS User manual

From any page of the BIPASS site, you may return to BIPASS homepage (http://bip.umiacs.umd.edu:8080/ ) by clicking on either the New Search link or HOME link (located at the top of the flash menu bar).

List of BIPASS Services

Two services are currently available:

1- BIPAS-SpliceDB Service provides AS information extracted from various public resources.

2- BIPAS-Align&Splice Service computes AS information from your own transcript sequences and selected genome

BIPASS frontpage (see Figure 1 below), displays a form that gives access to both services: BIPAS‑SpliceDB on the left and BIPAS-Align&Splice on the right.

Note that these are different services. BIPAS-SpliceDB provides access to a data warehouse that we generated from public resources. In contrast, BIPAS-Align&Splice allows the submission of transcripts that may not be registered in public resources, align them against the selected genomic data and performs AS analysis. The whole pipeline is achieved on-line for transcripts submitted to BIPAS-Align&Splice and will return less annotation than queries against BIPAS-SpliceDB.

Figure 1: Homepage BIPAS services

Selection of the service

The service is selected as follows. To access the information stored in the BIPAS-SpliceDB, select “Search transcripts for Genes” located on the left side of the form. To submit sequences to BIPAS‑Splice&Align, select “Submit sequences to search for AS events”.

BIPAS-SpliceDB

On the left side, the form providing access to BIPAS–SpliceDB is composed of 3 fields, “for”, "Using” and “in organism”. To perform a search, you enter one keyword in the field “for”, choose the most appropriate “using” field (GenbankID or Annotation), and select the genome with “in organism” (Human or Mouse). If no selection is made, the service uses defaults parameters: “Any Field” and “Any” respectively. The Search is Case insensitive but does not allow the use of a wildcard.

Note that the current version of BIPAS-SpliceDB (April 2007) does not allow queries against other field than annotation. Because gene information (including gene name) is not provided by resources integrated by the pipeline to constitute the data warehouse SpliceDB, the field Annotation will not access gene information. A user typing a gene name if the Annotation field will probably be returned several clusters for which the gene name appears in the annotation of gene related transcripts. A future version of the service will allow the retrieval of the gene cluster given a gene name. Sequences are not access by the field annotation, therefore a user entering a transcript sequence in the field annotation will not be returned an output either. Users interested in extending the scope of search criteria are welcome to contact BIP_FEEDBACK@asu.edu.

Input of Keywords

Example:

For: CDKN1

Using Annotation

In organism: Human

Figure 2: Search Inputs

Once the form is completed, clicking on the GO button will display the page shown is Figure 3.

Figure 3: Page of Clusters Results

BIPAS-SpliceDB service returns a clickable table. The user’s query is shown above the results table (top left). The first row of the table indicates the total number of clusters found in the database (here 9 clusters), and the time needed to answer the query (8 seconds). The second row lists information related to each cluster: the number of clones it contains, the clone identifiers, the number of genomic exons, and whether it contains variants, and information related to the chromosome: identifier, orientation, beginning, and end, and the organism. The following rows displays information related to each cluster matching the user’s query. Once you have found the cluster of interest, you can click on it.

For example, you can click on the cluster “Hs.chr6.17383” (see red arrow in Figure 3) to get more details about the cluster such as its transcripts, exons, introns, associated splice graph, etc. Clicking on the cluster link brings up the page shown in Figure 4:

Figure 4: Cluster Information Page

The Cluster page may be divided in two components: the table and the clickable graph which give information about the transcripts in the cluster.

The Cluster table information

The table displays information about the cluster such as genome and chromosome information. Transcript and genomic information may be see only by clicking links in the column “view” (red square in Figure 4) or download information in Text or/and XML format (blue square in Figure 4). For example, you can get details on the sequence of genomic exons by clicking on the link: view genomic Exon Sequences that displays the page shown in Figure 5.

Figure 5: Genomic Exon Sequences per Exons

Cluster Graph

Figure 6: Cluster Graph

The Cluster graph consists of a legend (blue rectangle) and transcript information (violet rectangle). No clickable link exists in the legend part. In the graph, exons and introns of the genomic sequence and of each transcript are clickable and lead to their respective nucleotide sequence. Each code for a transcript on the left of the clickable graph (red rectangle in the Figure 6 above) points to transcript annotations and a graphical representation of the transcript.

Click on genomic Sequence

By clicking on the title “genomic sequence”, a page displaying all the genomic sequence of the cluster with exons and introns is obtained (see Figure 7).

Figure 7: Genomic Sequence of a Cluster

Clicks on exon and intron

A click on an exon or intron points directly to its nucleotide sequence in a page containing all the genomic exonic sequences for the genomic data as shown in Figure 8. If you click on an exon or intron of a transcript, you will access to the specific exon or intron of the transcript from the page dedicated to all the information about the transcript itself (See Figure 10).

Figure 8: Genomic Exonic Sequence - Example

Click on transcript Codes

By clicking on the code of a transcript such as NM_000389 (see red arrow in Figure 9), a new page containing all information about the transcript is displayed (see Figure 10). It contains annotations, information about exons and introns, and a graphical representation of the transcript. At the top of the page, links to download transcript information (with or without the graph) exist in two formats: XML or text format.

Figure 9: Clickable Transcript Codes

… …

Figure 10: Transcript Information Page

BIPAS-Align&Splice, sequences submission service

To submit transcripts sequences and find AS events in them, select the radio button on the right side of the form (see red arrow in Figure 11) and click on the Go Button on (see green arrow)

Figure 11: BIPASS Submission

Once the BIPAS-Align&Splice service is selected, the form shown in Figure 12 is displayed. The completion of the submission is a three-step process (see the number on the left part of the tables).

I. Enter transcript Sequence

II. Select or Enter Genomic Data

III. Enter a valid e-mail address

Note that the service does not provide access to the data warehouse SpliceDB. Instead it computes the AS analysis on line. It allows users to submit their own sequences for AS analysis.

Figure 12: Inputs of Submission

How to Submit Transcript Sequences?

There are two different ways to submit transcript sequences (Paste Sequence or Upload sequences from a file) and two different formats that can be used (FASTA[1] or Genbank[2] Format).

You can submit several transcript sequences at the same time.

In FASTA format the sequences must be separated by a blank line both in paste system or in the file used to upload sequences. In the Genbank Format, the separation is a carriage return, double slash (//) and carriage return.

NOTE: Click on a text area or on the Browse button automatically selects the appropriated radio button for the paste or upload selections but not for the File Format.

By default, the FASTA Format is selected. If you use the GenBank format, select it before you click on the GO Button.

Table of Contents:

List of Figures:

Access to BIPASS home page