GMAJ
Annotations
  • [+]All
    • [+]MAF File
      • Invalid MAF version (maf_version)
      • Skipping unsupported paragraph (maf_paragraph)
      • Skipping all reconstruction scores: no species specified (recon_noseq)
      • Skipping reconstruction scores in blocks with missing row (recon_missing)
      • The first row in some blocks is not the specified reference sequence (refseq_not_first)
      • Skipping extra MAF File (unused_maf)
    • [+]Annotation Files
      • [+]Semantic Assumptions
        • [+]BED Format
          • BED12 blocks are exons (bed_blocks)
          • BED thickstart/thickend designate CDS (bed_thick)
          • BED name is gene name when loading exons from BED12 (bed_name)
          • BED name is gene name when loading exons from exon BED (bed_name_full)
          • BED name's prefix is gene name when loading exons from exon BED (bed_name_prefix)
        • GFF group is gene name (gff_group)
      • [+]Skipped Items
        • Skipping lines in unrecognized format (annot_format)
        • Skipping lines with no gene name when loading exons (gene_missing)
        • Skipping lone CDS start/stop codons when strand is unknown (ambiguous_codon)
        • Skipping lines with invalid repeat types (unrec_repeat)
        • Using 'Other' for missing or incomplete repeat types (repeat_type_missing)
        • Ignoring invalid strand fields (bad_strand)
        • Ignoring invalid score fields (bad_score)
        • Ignoring invalid color fields (color_format)
        • Ignoring malformed URLs (bad_url)
        • Score shading is not yet supported (score_shading)
      • [+]Red Flags
        • Sequence name in annotation file does not match name in MAF (seqname_mismatch)
        • BED start or end < 0 (bed_coord)
        • GFF start or end < 1 (gff_coord)
        • Missing item name for URL substitution (url_subst)
    • [+]Miscellaneous
      • No refseq specified; assuming 'first' (default_refseq)
      • One or more bundle entries are not used in parameters file(unused_entry)
      • Skipping blocks for export where reference sequence is hidden or all gaps (export_skip)
      • Possible parse error: token ends with an escaped quote (escaped_quote)
      • Draggable panel dividers will not be sticky (no_sticky)
These do not affect behavior, only suppress warning messages.

You can use this tool to view a set of MAF alignments. You may also include optional annotation data for one or more of the organisms.

For detailed information on GMAJ, click here.

Gmaj is a tool for viewing and manipulating Generalized Multiple Alignments (GMAs) produced by programs such as TBA (though it can also be used with maf-format alignments from other sources). It can display interactive graphical and text representations of the alignments, a diagram showing the locations of exons and repeats, and other annotations -- all with the user's choice of reference sequence.