Download sequences

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RELEASE NOTES

This version is the most recent stable release of the medicago genome.

DOWNLOADS

• Genome Assembly: Files containing all the Mt3.5.2 sequences alongwith all the pseudo-golden paths used to create the assemblies.
• MedtrA17_3.5.assemblies.fasta FASTA formatted sequences of the 8 chromosomes, 146 unanchored BACs plus Illumina contigs that are not placed on the chromosomes
• MedtrA17_3.5.assemblies.agp GenBank Accessioned Golden Path (AGP) files describing the assembly of each chromosome
• Mt3.5.1_all_BACs.fa.tar.gz FASTA format sequences for all of the 2533 BACs used in the assemblies (contains 8 BACs from Chr5 which were not in GenBank yet)
• MT_all_BAC_ends.fa.tar.gz FASTA format sequences of Medicago BAC ends
• Genome Annotation: Gene predictions in FASTA and MIPS GFF formats
• Mt3.5v5_GenesProteinSeq_20111014.fa Mt3.5v5 Annotation Protein Fasta files
• Mt3.5v5_GenesCDSSeq_20111014.fa Mt3.5v5 Annotation CDS Fasta files
• Mt3.5v5_GenesTranscriptSeq_20111014.fa Mt3.5v5 Annotation Spliced and Unspliced Transcript Sequences Fasta files
• Mt3.5v5_genes_20111014_MIPSGFF.gff MIPS GFF formatted file for GENES on Chr01 - Chr08, unanchored BACs and Illumina contigs (entire proteome)
• Mt3.5v5_TEs_20111014_MIPSGFF.gff MIPS GFF formated file for TRANSPOSABLE ELEMENTS on Chr01 - Chr08 plus unanchored BACs
• Mt3.5v4_tRNA_20111222.gff MIPS GFF formated file for tRNA on Chr01 - Chr08 plus unanchored BACs

>>> CLICK HERE TO VISIT THE FTP DOWNLOAD PAGE <<<

RELEASE NOTES

This version contains the dataset described in the Medicago truncatula Genome paper, published in the journal Nature.

DOWNLOADS

• Genome Assembly: Files containing all the Mt3.5.2 sequences alongwith all the pseudo-golden paths used to create the assemblies.
• MedtrA17_3.5.assemblies.fasta FASTA formatted sequences of the 8 chromosomes, 146 unanchored BACs plus Illumina contigs that are not placed on the chromosomes
• MedtrA17_3.5.assemblies.agp GenBank Accessioned Golden Path (AGP) files describing the assembly of each chromosome
• Mt3.5.1_all_BACs.fa.tar.gz FASTA format sequences for all of the 2533 BACs used in the assemblies (contains 8 BACs from Chr5 which were not in GenBank yet)
• MT_all_BAC_ends.fa.tar.gz FASTA format sequences of Medicago BAC ends
• Genome Annotation: Gene predictions in FASTA and MIPS GFF formats
• Mt3.5v4_GenesProteinSeq_20110616.fa Mt3.5v4 Annotation Protein Fasta files
• Mt3.5v4_GenesCDSSeq_20110616.fa Mt3.5v4 Annotation CDS Fasta files
• Mt3.5v4_GenesTranscriptSeq_20110616.fa Mt3.5v4 Annotation Spliced and Unspliced Transcript Sequences Fasta files
• Mt3.5v4_genes_20110616_MIPSGFF.gff MIPS GFF formatted file for GENES on Chr01 - Chr08 plus all extra BACs
• Mt3.5v4_TEs_20110616_MIPSGFF.gff MIPS GFF formated file for TRANSPOSABLE ELEMENTS on Chr01 - Chr08 plus all extra BACs
• Mt3.5v4_tRNA_20111222.gff MIPS GFF formated file for tRNA on Chr01 - Chr08 plus all extra BACs
• Mt3.5v4IlluminaGenes_20110621_MIPSGFF.gff MIPS GFF formatted file for GENES on Illumina Contigs

>>> CLICK HERE TO VISIT THE FTP DOWNLOAD PAGE <<<

RELEASE NOTES

This version corresponds to the release, subsequent to the rebuilding of the pseudomolecules using the Optical Map.

DOWNLOADS

• Genome Assembly: Files containing all the Mt3.5.1 sequences alongwith all the pseudo-golden paths used to create the assemblies.
• Mt3.5.1_pseudomolecules.tar.gz FASTA formatted sequences of the pseudomolecules and 146 unanchored BACs
• Mt3.5.1_gb_files.tar.gz Preliminary GenBank Accessioned Golden Path (AGP) files describing the assembly of each chromosome
• Mt3.5.1_all_BACs.fa.tar.gz FASTA format sequences for all of the 2533 BACs used in the assemblies (contains 8 BACs from Chr5 which were not in GenBank yet)
• Mt_all_BAC_ends.fa.tar.gz FASTA format sequences of Medicago BAC ends
• Genome Annotation: IMGAG gene predictions in FASTA, MIPS GFF and TIGRXML formats
• Mt3.5_TIGRXMLs_20100825.tgz TIGRXML files of Chr01 - Chr08 plus all extra BACS
• Mt3.5v3_annotation_files.tar.gz Mt3.5v3 Annotation Fasta files (Protein, CDS, Spliced and Unspliced transcript sequences
• Mt3.5_genes_20100825_MIPSGFF.gff MIPS GFF formatted file for GENES on Chr01 - Chr08 plus all extra BACs
• Mt3.5_transposons_20100825_MIPSGFF.gff MIPS GFF formated file for TRANSPOSABLE ELEMENTS on Chr01 - Chr08 plus all extra BACs
• Mt3.5_tRNA_20100723_MIPSGFF.gff MIPS GFF formated file for tRNA on Chr01 - Chr08 plus all extra BACs

>>> CLICK HERE TO VISIT THE FTP DOWNLOAD PAGE <<<

Version 3.0 was generated before the pseudomolecules were rebuilt, and should only be used for tracking purposes. This data has been deprecated. Use with caution.

RELEASE POLICY

The Medicago Genome Sequence Consortium (MGSC) is pleased to release assembly Mt3.0. This assembly may be freely downloaded, used in analyses and repackaged in databases with appropriate attribution and with the following conditions:

• Users are free to use the data in scientific papers analyzing specific genes and genome regions provided that the MGSC is properly acknowledged.
• The MGSC reserves the right to publish the initial large-scale analyses of the dataset including large-scale characterization of regions of evolutionary interest and large-scale genomic assembly. Large-scale refers to regions of size 1Mbp or more.
• Mt3.0 is incomplete and should be regarded as preliminary. Data characteristics and limitations are described in the README and Medicago Fact Sheet

DOWNLOADS

• Genome Assembly: Files containing all the Mt3.0 sequences (8 pseudomolecules and 148 unanchored BACs) alongwith all the pseudo-golden paths used to create the assemblies.
• Mt3.0_pseudomolecules.tar.gz FASTA formatted sequences of the pseudomolecules and 148 unanchored BACs
• Mt3.0_pgp_files.tar.gz Pseudo-golden path files describing the assembly of each chromosome
• Genome Annotation: IMGAG gene predictions in FASTA, MIPS GFF and TIGRXML formats
• Mt3.0_cds_20090702_NAMED.fa.tar.gz FASTA formatted coding sequences for IMGAG annotated genes
• Mt3.0_proteins_20090702_NAMED.fa.tar.gz FASTA formatted protein sequences for IMGAG annotated genes
• Mt3.0_20090702_MIPSGFF.gff Annotation in MIPS GFF format
• MT3_TIGRXMLs_20091012.tgz Annotation in TIGRXML format