The set of allelic genes found in multiple individuals in a species or closely related species may be called a "pangene set," with the gene models that correspond by homology and position being called a pangene. The pangene set calculated for Glycine accessions at SoyBase can be used to find corresponding genes across assemblies and annotations.
-- There are several good options for identifying corresponding genes in different accessions or annotations. If you have ... - -
+ The set of allelic genes found in multiple individuals in a species or closely related species may be called a "pangene set," + with the gene models that correspond by homology and position being called a pangene. The pangene set calculated + for Glycine accessions at SoyBase can be used to find corresponding genes across assemblies and annotations. +
++ If you have one or several (fewer than 100) genes to look up, use the Pangene Lookup tool below. + This page accepts a list of genes (separated by spaces or line returns). +
+ +If you have hundreds or thousands of genes to look up, you can download a correspondence table for either + + the reference lines, + + or for + + a correspondence table for all pangene accessions. + +
+ + +Using the + the reference lines + as an example, the data is organized by genes (rows) and annotation-versions (columns). +
+| Pangene ID | +Wm82.gnm1.ann1 / Wm82.a1.v1 | +Wm82.gnm2.ann1 / Wm82.a2.v1 | +Wm82.gnm4.ann1 / Wm82.a4.v1 | +Wm82.gnm6.ann1 / Wm82.a6.v1 | +more | +
|---|---|---|---|---|---|
| {{ name.pangene }} | +{{ name.glyma_Wm82_gnm1_ann1 }} | +{{ name.glyma_Wm82_gnm2_ann1 }} | +{{ name.glyma_Wm82_gnm4_ann1 }} | +{{ name.glyma_Wm82_gnm6_ann1 }} | +{{ name.more }} | +
+ To work with either of these files, uncompress it, then open it using Excel or similar spreadsheet program;
+ or if you have a little familiarity with a Unix terminal, you can extract data in many ways (a few examples):
+
cat Glycine.pan5.MKRS.table_ref_lines.tsv | tr '\t' '\n' # to see the list of headers
cut -f1,2,8,10 Glycine.pan5.MKRS.table_ref_lines.tsv | head # to see four selected columns (the first 10 entries)
grep -f YOUR_LIST_OF_GENES.txt Glycine.pan5.MKRS.table_ref_lines.tsv # to search a provided list of gene IDs against the file
- cat Glycine.pan5.MKRS.table.tsv | head -1 | tr '\t' '\n' # to see the list of headers - cut -f1,2,8,10 Glycine.pan5.MKRS.table.tsv| head # to see four selected columns (the first 10 entries) - grep -f YOUR_LIST_OF_GENES.txt Glycine.pan5.MKRS.table.tsv # to search a provided list of gene IDs against the file --
Sample data from the - - correspondence table for the reference lines: - -
-| Pangene ID | -Wm82.gnm1.ann1 / Wm82.a1.v1 | -Wm82.gnm2.ann1 / Wm82.a2.v1 | -Wm82.gnm4.ann1 / Wm82.a4.v1 | -Wm82.gnm6.ann1 / Wm82.a6.v1 | -more | -
|---|---|---|---|---|---|
| {{ name.pangene }} | -{{ name.glyma_Wm82_gnm1_ann1 }} | -{{ name.glyma_Wm82_gnm2_ann1 }} | -{{ name.glyma_Wm82_gnm4_ann1 }} | -{{ name.glyma_Wm82_gnm6_ann1 }} | -{{ name.more }} | -
The method for generating the pangene correspondences is described briefly here:
+ + +The Pandagma software package (Cannon, Lee, Weeks, Berendzen) was used to identify pangene and gene family sets. + The main steps in Pandagma's pangene process are:
+The Pandagma package is available at https://github.com/legumeinfo/pandagma, including the configuration used to calculate the pangene data above.
+ +The pangene collection for Glycine, including data in several formats and descriptions of the fies, is in the "Glycine/GENUS/pangenes" section of the Data Store.
+ +If you have extensive programmatic work and need to translate among arbitrary accessions, + the gene_translate.pl + utility in pandagma may be helpful. +
+The gene correspondences in the lookup tables above were calculated using the -Pandagma package for identifying pangenes from a given collection of annotations. -The method is described briefly here:
- - -The Pandagma software package (Cannon, Lee, Berendzen) was used to identify pangene and gene family sets. The main steps in Pandagma's pangene process are:
-The Pandagma package is available at https://github.com/legumeinfo/pandagma, including the configuration used to calculate the pangene data above.
- -The pangene collection for Glycine, including data in several formats and descriptions of the fies, is in the "Glycine/GENUS/pangenes" section of the Data Store.
- -If you have extensive programmatic work and need to translate among arbitrary accessions, - the gene_translate.pl - utility in pandagma may be helpful. -
+