Conserved Orthologs in Plants (Arabidopsis Single Copy Genes)


Download raw data

Sequences in FASTA format:

Arabidopsis:

    ath_NCBI_cds.fasta.nr.info
    ath_NCBI_genes.fasta.nr.info

    arabidopsis_single_copy_genes.fasta

Other Plants:

    cos_lettuce.fasta
    cos_maize.fasta
    cos_rice.fasta
    cos_soybean.fasta
    cos_sunflower.fasta (CGPDB only)
    cos_sunflower_all.fasta (CGPDB + all others)
    cos_tomato.fasta

arabidopsis_single_copy_genes_2003.html - graphical data representation

sequences were derived using following pipeline:


Alignments with Arabidopsis at nucleotide level
(no gaps, no stop codons):

Detailed description of the alignment extraction protocol

    cos_lettuce.align.tar.gz
    cos_maize.align.tar.gz
    cos_rice.align.tar.gz
    cos_soybean.align.tar.gz
    cos_sunflower.align.tar.gz (CGPDB only)
    cos_sunflower_all.align.tar.gz (CGPDB + all others)
    cos_tomato.align.tar.gz

Alignment Overlap Info:

    cos_lettuce.codons.overlap_info
    cos_maize.codons.overlap_info
    cos_rice.codons.overlap_info
    cos_soybean.codons.overlap_info
    cos_sunflower.codons.overlap_info (CGPDB only)
    cos_sunflower_all.codons.overlap_info (CGPDB + all others)
    cos_tomato.codons.overlap_info

Sequences containing ORFs extracted from BLASTX report:
   
"Query" sequences (EST ORFs)
 "Subject" sequences (Arabidopsis ORFs)
cos_lettuce.codons.query_seq
 cos_lettuce.codons.subj_seq
cos_maize.codons.query_seq
 cos_maize.codons.subj_seq
cos_rice.codons.query_seq
 cos_rice.codons.subj_seq
cos_soybean.codons.query_seq
 cos_soybean.codons.subj_seq
cos_sunflower.codons.query_seq
 cos_sunflower.codons.subj_seq
cos_sunflower_all.codons.query_seq
 cos_sunflower_all.codons.subj_seq
cos_tomato.codons.query_seq
 cos_tomato.codons.subj_seq


Multiple alignments: lettuce - sunflower - Arabidopsis at DNA level, ORFs only:

Alignments for all potential orthologs in one file: overlapping_seqs_all_let_sun_ath.txt

Alignments for all potential orthologs in one directory (each alignment in a separate file): overlapping_seqs_all_let_sun_ath.dir.tar.gz

Alignments for all conserved orthologs in one file: overlapping_seqs_cos_let_sun_ath.txt

Alignments for all conserved orthologs in one directory (each alignment in a separate file): overlapping_seqs_cos_let_sun_ath.dir.tar.gz


Alignments were derived using overlap_finder_017.py Python script. To see details of script usage click here

email: akozik@atgc.org
last modified: November 20 2003