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PlantIGB - What data are available?

By default, PlantIGB accesses the PlantQuickload data web site hosted at http://www.bioviz.org/plant_quickload.

The PlantQuickload Web site is just a set of directories (folders) on our server that IGB can access and load via the Internet. If you are a computational biologist interested in doing data-mining experiments with Arabidopsis data, the files in these directories may be very useful. Be sure to read the README.html file(s) for notes on formats and other topics. And if you have questions, send us an email: aloraineuab.edu.

The data files currently available in PlantQuickload include the following:

Arabidopsis thaliana

• TAIR version 7 annotations.
• TAIR version 7 EST & cDNA alignment annotations
• ESTs from the Salk SIGnal site
• ATH1 probeset-to-genome alignments from Affymetrix
• TAIR version 6 annotations
• TAIR version 5 annotations
• Genomic sequence

TAIR version 7 annotations

These data all are from the file named TAIR7_GFF available from The Arabidopsis Information Resource (TAIR) ftp site, downloaded in April, 2007.

To load data into IGB, click the checkboxes under the Data Access tab. Each data set will appear in a separate track. To find out more about a particular annotation, right-click the annotation (or control-click on Mac) and select the arabodopsis.org option, which should tell your Web browser to open the corresponding locus page at TAIR. The new page should tell you what the category ("Gene Model Type") the gene belongs to -- these should match the tier label in IGB.

TAIR version 7 EST and cDNA alignments

To find out more about the computational pipeline that generated these alignments, visit the Genome Annotation page at TAIR, which describes how the alignment pipeline operates.

These data are from the TAIR ftp site (see: ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR7_pre-release/TAIR7_Transcripts_by_map_position) These correspond to the "transcripts" tier in the TAIR on-line seqviewer (genome browser) tool.

    Fields:

    0 Locus - AGI locus code
    1 Locus_orientation_is_5 - gene orientation relative to genomic sequence 
    2 Genbank_acc - Genbank accession
    3 external_id - Genbank gi number
    4 Type(1=cDNA_2=EST)
    5 Chromosome number (6 is chloroplast, 7 is mitochondrion)
    6 Transcript_orientation_is_5 - transcript orientation relative to genomic sequence

Note that a 3-prime EST will likely appear on the opposite
strand from the associated gene.

    7 Map_start_coordinate - one-based
    8 Map_end_coordinate - one-based

For visualization in IGB, we subdivided the EST and cDNA alignment annotations into two new annotation subsets based on the number of map positions TAIR has reported for a single expressed sequence:

IGB menu name: EST_TAIR7mm - TAIR7 ESTs that map to more than one location in the genome. (The suffix "mm" stands for multi-mapper.)

IGB menu name: EST_TAIR7sm - TAIR7 ESTs that map to more than one location in the genome. (The suffix "sm" stands for single-mapper.)

EST-2006-12-19.txt 12-Mar-2007 12:54 14M

ATH1 probeset-to-genome alignments from Affymetrix

This data set contains ATH1 probeset-to-genome alignments from Affymetrix. Note that numerous probe sets align to the genome in multiple locations. We have not yet done any quality-testing or screening to sort out why this is the case, but hope to do so in future.

Redman, et al (2004) Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.

Note that probes typically occupy positions near the three-prime end of the design sequences, with some exceptions.

The data shown in IGB are from a data file provided by Affymetrix. The file from Affymetrix uses a data representation format that captures gaps or insertions in the design sequence relative to the genomic sequence. When you examine the probe set alignments in IGB, you may see immediately adjacent or overlapping blocks in some probe sets. This means that a portion of the design sequence is missing the in the genomic sequence and corresponds to a gap in the genomic sequence relative to the design sequence. Note also that some probes overlap with each other; this is quite common.

You can obtain a copy of the ATH1 probe set alignments from the "Support" section of the Affymetrix Web site. It is likely to be identical to the version posted here.

TAIR version 6 annotations

TAIR version 5 annotations

Genomic sequence

The sequence data are from:

ftp://ftp.arabidopsis.org//home/tair/home/tair/Sequences/whole_chromosomes

and are identical to the Genbank versions listed below, except for the mitochondrial sequence file, which differed in length by one base.

Sequence data files

The IGB "bnib" files are compressed versions of the sequence data files. They are a compressed to reduce the amount of time it takes them to load when you click the "Load all sequence" button under the "Data Access" tab in IGB.