GMAJ
Annotations
  • [+]All
    • [+]MAF File
      • Invalid MAF version (maf_version)
      • Skipping unsupported paragraph (maf_paragraph)
      • Unrecognized character found in alignment (bad_char_all)
      • 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
        • Assuming that annotations in file ___ are for species ___ (seqname_fix_all)
        • 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)
      • Selecting a large block may be very slow (big_block)
These do not affect behavior, only suppress warning messages.

Reference Sequence: The default option, "First sequence in each block", is the correct choice for the vast majority of MAF alignments. The alternative, "Any sequence", will allow you to flip the blocks to view them with any of the MAF sequences as the reference, but this is only appropriate if the file was generated by a sequence-symmetric alignment program such as TBA. Using "Any sequence" with an ordinary MAF will not give the same results as if that alignment had been run with a different reference sequence.

Annotation Style: The default style, "Galaxy", specifies one set of annotations for each species in the MAF file; it assumes that if you have, say, exons for several chromosomes of one species, they are all together in one file. The other style, "Basic", is more flexible but cumbersome: a separate set of files is specified for each sequence (e.g. chromosome), and you must fill in the full sequence name as it appears in the MAF. The Basic style also allows you to provide a display offset that GMAJ will add to all of the position labels for that sequence. With either style, specifying more than one set of annotations for the same sequence will result in an error message from GMAJ.

What it does

GMAJ is an interactive viewer for MAF alignments, with support for optional annotation data. In addition to browsing the alignments, you can select and export them according to a variety of criteria and send the output back to your Galaxy history.

For detailed information on GMAJ, click here.