/PrimateMultigeneFamilySearch

Search paralog ortholog database to construct multigene families in primates

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PrimateMultigeneFamilySearch

Search paralog ortholog database to construct multigene families in primates

Two lists of 2-paralog multigene families:

  1. A less careful list that combining Duplicated Genes Database and OrthoMAM Database. This list has 113 pairs of genes.

  2. List from above being selected with metaPhors database. This list has 8 pairs of genes left.

DNA CDS sequences were obtained from OrthoMAM v9 that contain 5 primate species:

  1. Homo sapiens
  2. Pan troglodytes
  3. Gorilla gorilla
  4. Pongo abelii
  5. Macaca mulatta

Now, add Callithrix (NCBI taxonomy id 9583) as outgroup. The two lists after this step have:

  1. Less accurate list has 104 pairs of genes left.
  2. More careful list has 7 pairs of genes left.

Note:

In STEAP4_STEAP2.fasta, MacacaSTEAP4 was added G in the end of sequence to complete the stop codon manually.

CNTN6 CNTN4 pair was removed.

In IGSF3_CD101.fasta, PongoIGSF3 was added A in the end of sequence to complete the stop codon manually.