Computational protocol: Differential roles of TGIF family genes in mammalian reproduction

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Protocol publication

[…] Human genomic sequences for TGIFLX, TGIF2 and TGIF1 were obtained from the UCSC genome browser http://genome.ucsc.edu/. The conserved block of genes surrounding these loci were identified in amniote species using the VISTA genome browser program http://pipeline.lbl.gov/cgi-bin/gateway2. Blast was then performed in mouse, opossum, platypus, lizard, frog, fugu and fly. Genomic sequence from these orthologous blocks was also obtained from UCSC and aligned using the LAGAN algorithm available on the mVISTA website with default parameters http://genome.lbl.gov/vista/mvista/submit.shtml except that TGIFLX orthologues were aligned with PROLAGAN algorithm. In an attempt to identify any TGIFX orthologues in marsupials or platypus we performed a low stringency BLAST using the individual human TGIFX exons as well as a protein BLAT. In each case no homology was found.Searches for homologues of TGIF1, TGIF2 and TGIFLX/Y were performed at NCBI http://www.ncbi.nlm.nih.gov and Ensembl http://www.ensembl.org and orthologues were found in eutherians, marsupials, monotreme (platypus), birds and reptiles, fish and invertebrates (fruit fly and mosquito) (Additional file , Table S1). Phylogenetic analysis was performed with PHYLIP 3.69 program with default parameters (University of Washington) using neighbour-joining analysis with 100 replicates, and viewed with TREE-view 1.66 http://taxonomy.zoology.gla.ac.uk/rod/treeview.html. […]

Pipeline specifications

Software tools mVISTA, BLAT, PHYLIP, TreeViewX
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Mus musculus, Homo sapiens