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ExonMapper

[Introduction] [Sequence Selection] [Parameters] [Program Output]

Introduction

Large scale exon-mapping becomes more and more attractive because of

and

cDNA sequences provide the protein sequences, but exon-mapping also reveals the gene structure and possibly locates the promoter of full length cDNAs. Large amounts of data require non-interactive methods that also tolerate frame shifts and partial sequences.

Genomatix'ExonMapperis a tool to fulfill these requirements:

ExonMapper Input Data

Sequence Selection
Enter the mRNA/cDNA sequences Enter a set with at least one mRNA/cDNA sequence.

mRNA/cDNA sequences are assumed to be in 5'- 3' direction. All sequences in the set must have the same format. For a description of the available sequence formats see thesequence help page
Enter the genomic DNA sequences Depending on the selected task, you will have to enter a set of genomic DNA sequences (task "Exon mapping on your sequence(s)") or select a database (task "Exon mapping against database"):
  • Enter a set of genomic DNA sequences: All sequences in the set must have the same format. For a description of the available sequence formats see the sequence help page
  • Select a database: For a description of the database access see the list of available databases
ExonMapper parameters
Hits
  • Maximum number of results.
    Enter the maximum number of mapping results that shall be listed in the output. Only the best results are listed.

  • Minimum average exon alignment quality.
    Enter the minimum average percentage of perfect matches in exon alignments.

  • Minimum percentage of aligned mRNA. Enter the minimum percentage of mRNA which must be mapped on a genomic sequence.
Email address Here you can choose between two methods for receiving the results:
  • Show result directly in browser window
    In this option the URL of the result is directly shown in your browser window.

    Warning: Please use this option only for analyses which can be performed in a short time.
    If the analysis takes longer than the timeout of the webserver, the connection will be terminated and you will receive an error message (e.g. "The document contained no data."). In this case, the results will not be available, please restart the analysis using the option below "Send the URL of the result to".

  • Send the URL of the result via email
    In this option an email with the URL of the results will be sent to the user provided email address, when the analysis is finished.

The results will be available for a limited time on our server. For details of how long your results will be kept please see the result-email. After that period they will be deleted unless protected in the project management!

Program Output

ExonMapper will create an output file with

Here is an example output for the exon mapping of a Human mRNA sequence for cytoskeletal gamma-actin (HSACTCGR) and a Human mRNA for actin-binding protein (filamin) (ABP-280) to the human genome, NCBI release 35.

ExonMapper Release 3.5 Jan 2005

ExonMapper Parameters:

mRNA/cDNA
Accession number: X04098, X53416 (2 seq.)
genomic
Sequence file: Human Complete
Max. # reported hits:
10
Average Exon alignment quality:
90 %
Min. overlap mRNA/genomic sequence:
60 %

mRNA/cDNA input sequences

Name AC Length Description
HSACTCGR [X04098] (1918 bps) Homo sapiens mRNA for cytoskeletal gamma-actin (ACTG1 gene).
HSABP280 [X53416] (8368 bps) Human mRNA for actin-binding protein (filamin) (ABP-280).

mRNA/cDNA input sequence HSACTCGR [X04098] (1918 bps)

Search results: [Genomic sequences]

Search for genomic sequences:

Mapped mRNA/cDNA HSACTCGR on one genomic sequence

Name AC Length Description #Exons mRNA overlap Exon alignment
NT_024871 [NT_024871] (2103126 bps) Homo sapiens chromosome 17 genomic contig. 6 100 % 100 %

Exon mapping:

Mapped 6 Exons from mRNA/cDNA sequence HSACTCGR [X04098] antisense strand on genomic sequence NT_024871 [NT_024871] (2103126 bps)

Info: 100 % of the mRNA/cDNA sequence were aligned with 100 % similarity

Exon mRNA/cDNA genomic sequence Warnings
Begin End Length Begin End Length
Exon 1 1 67 67 bps 1883365 1883299 67 bps -----
Exon 2 68 196 129 bps 1882925 1882797 129 bps -----
Exon 3 197 436 240 bps 1882707 1882468 240 bps -----
Exon 4 437 875 439 bps 1882191 1881753 439 bps -----
Exon 5 876 1057 182 bps 1881673 1881492 182 bps -----
Exon 6 1058 1918 861 bps 1881398 1880538 861 bps -----

Alignments

Splice sites are marked red
Overlapping mRNA/cDNA alignments are marked green
Mismatches are marked blue

mRNA/cDNA input sequence HSABP280 [X53416] (8368 bps)

Search results: [Genomic sequences]

Search for genomic sequences:

Mapped mRNA/cDNA HSABP280 on one genomic sequence

Name AC Length Description #Exons mRNA overlap Exon alignment
NT_025965 [NT_025965] (1015171 bps) Homo sapiens chromosome X genomic contig. 48 100 % 99 %

Exon mapping:

Mapped 48 Exons from mRNA/cDNA sequence HSABP280 [X53416] antisense strand on genomic sequence NT_025965 [NT_025965] (1015171 bps)

Info: 100 % of the mRNA/cDNA sequence were aligned with 99 % similarity

Exon mRNA/cDNA genomic sequence Warnings
Begin End Length Begin End Length
Exon 1 1 56 56 bps 954892 954837 56 bps -----
Exon 2 57 545 489 bps 951692 951204 489 bps -----
Exon 3 546 794 249 bps 948421 948173 249 bps -----
Exon 4 795 892 98 bps 948069 947972 98 bps -----
...
Exon 45 7329 7505 177 bps 930538 930362 177 bps Point mutations: 1
Exon 46 7506 7724 219 bps 930198 929980 219 bps -----
Exon 47 7725 7928 204 bps 929896 929693 204 bps -----
Exon 48 7929 8368 440 bps 929367 928928 440 bps Point mutations: 2

Alignments

Splice sites are marked red
Overlapping mRNA/cDNA alignments are marked green
Mismatches are marked blue


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