Contents

Reasons to convert

1. Only chromosome and optional scaffold sequences are processed.
2. Only the 'protein-coding' genes are processed.
3. Gene attributes:

   ID	From the input gene attributes.
   Name	From the input gene attributes (if it is not equal ID).
   desc	Is the gene description, where symbols (e.g. %3B) are replaced with the correct character. It removes the ending "[Source:..." from the input description.
   rnaID	Is equal to the first mRNA ID. Following the ID is (n), where n=number of mRNAs for the gene.
   proteinID	(optional) Is equal the 1st CDS protein-id of the 1st mRNA.

4. If it has problems converting the file(s), then symap will have problems loading them; the script can be edited for your particular files. (Note: Ensembl formats are not totally consistent, so xToSymap may not take everything into account).

Download

1. Go to Ensembl, which shows all species for which Ensembl has a genome. For plants and fungi, see EnsemblPlant and EnsemblFungi.
2. Select your species.
3. Select Download DNA sequence (FASTA).
   This takes you to a FTP site. It is recommended that you download the [prefix].dna_sm.toplevel.fa.gz, as it is the soft masked chromosome sequences.
4. Select the GFF3 from the Download genes, cDNAs, ncRNA, proteins - FASTA - GFF3 line.
   This takes you to an FTP site. Download the [prefix].gff3.gz file.

Multiple files: Ensembl allows individual chromosome FASTA and GFF files to be downloaded, hence, the ConvertEnsembl option (and script) will process all .fa (or .fa.gz) and .gff3 (or .gff3.gz) files in the directory.

1. Go to the symap_5/data/seq directory.
2. Make a subdirectory for your species and move the FASTA and GFF files into the directory.
3. Start the xToSymap program, select the appropriate options (described below), then select Convert. The FASTA file must end in ".fa" and the annotation file must end in ".gff3" (the Ensembl defaults). They may be zipped, i.e. have a '.gz' suffix.

data/seq/cabb/
      Brassica_oleracea.BOL.59.gff3.gz
      Brassica_oleracea.BOL.dna_sm.toplevel.fa.gz
      annotation/
         anno.gff
         gaps.gff
      sequence/
         genomic.fna

Rules: There are variations in the text associated with >seqid header lines. The rules used by this script are as follows:

1. If Only prefix is not blank, sequences are filtered out if the seqid does not start with the prefix. Then all the following apply to the non-filtered sequences:
    
2. Chromosomes: A sequence is considered a chromosome if: (a) the ">" is followed by a number, X, Y, or roman numeral, or (b) the header line contains the word 'chromosome'.
   • The exception is when the header line starts with '>Mt' or '>Pt', these will not be output unless Include Mt/Pt is selected.
   • Chromosomes are always output unless Only prefix is set, and the prefix does not match.
   • Output Seqid: If the ">" line contains 'chromosome N', where N={number, X, Y or roman numeral}, than this number is used. Otherwise, the word following 'chromosome' is used (e.g. C1).
   
   
3. Scaffolds: A sequence is considered a scaffold if the header line contains the word 'scaffold'.
   • They will only be output if Include scaffold is selected.
   • Output Seqid: 'Scaf' followed by a consecutive number.
   
   
4. Unknown: All other ">" entries are considered 'unknown'.
   • They will only be output if Only prefix matches the input header line seqid.
   • Output: Seqid: 'Unk' followed by a consecutive number.

1. Group prefix needs to be blank as there is no common prefix now.
2. Minimum size should be set to only load the largest scaffolds.

As of 23-July-2024, cabbage (Brassica_oleracea.BOL.dna_sm.toplevel.fa.gz) had 9 chromosome sequences and 32,877 scaffolds. If these were included in the converted output, Minimum size should be entered to reduce the number loaded. Calculate the Minimum size using the xToSymap Lengths button. It outputs all their sorted lengths followed by a summary table of lengths:

Seq#  Length      Seqid
    1  43,764,888  >C1
    2  52,886,895  >C2
    3  64,984,695  >C3
    4  53,719,093  >C4
    5  46,902,585  >C5
    6  39,822,476  >C6
    7  48,366,697  >C7
    8  41,758,685  >C8
    9  54,679,868  >C9
   10     550,871  >s01  Scaffold00285
   11     360,705  >s02  Scaffold00418
...(list rest of scaffolds with lengths)

Values for parameter 'Minimal length' (assuming no duplicate lengths):

#Seqs Minimum length
   10  550,871
   20  193,719
   30  152,041
   40  122,531
   50   98,180
   60   85,914
   70   70,524
   80   65,697
   90   61,049
  100   58,280

1. Check the projects you want to load, which will cause them to be shown on the right of the symap window.
2. For the project you want to load, open the project parameters window to enter the appropriate values.
3. The select Load Project.

1. Sequences are output according to the Option rules.
2. Gaps of >30,000 are written to the annotation/gap.gff file (this value can be changed in the xToSymap interface).

1. Only lines with the 'type' (3rd column) equal 'gene', 'mRNA' and 'exon' are read.
2. Genes with "biotype=protein_coding" are written to file, followed by the first mRNA and its exons.
3. All lines have their seqID replaced with that assigned when reading the FASTA file. They all have a modified set of attributes written.
4. The only gene attributes retained are ID, description and Name (if it is not the same as ID). It removes the ending "[Source:..." from the input description.