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Displaying 2 of 2 results for "FICD"
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Title Date Issued Date Released Description
Afrobatrachia_Sequence_Alignment
06-29-2016 06-29-2016
A nexus format sequence alignment of the five nuclear markers (FICD, KIAA2013, POMC, RAG1, TYR) and 16S data, along with relevant MrBayes style partitions and models defined. The alignment contains 186 taxa and 3700 bp.
Hyperoliid Orthologous Transcript Set
05-27-2016 05-27-2016
Marker set consisting of 1,265 orthologous transcripts (trimmed to 500-850 bp) from four species of hyperoliid frogs (5,060 total sequences). We compared annotated transcripts from the four species to search for orthologs via BLAST (Altschul et al. 1990). We removed mitochondrial loci from the transcripts. We only kept transcripts with a GC between 40%-70% because extreme GC content causes a reduced capture efficiency for the targets (Bi et al. 2012). Orthologous transcripts with a minimum length of 500 base pairs (bp) were identified across all four samples, resulting in the identification of 2,444 shared transcripts. Transcripts exceeding 850 bp were arbitrarily trimmed to this length for probe design, reflecting a trade-off decision between locus length and the total number of loci included in the experiment. The orthologous transcripts were subjected to additional filtering steps before a final gene set was chosen. The initial filtering step applied upper and lower limits on average transcript divergence, eliminating loci with low variation (< 5.0% average divergence) and exceptionally high variation (> 15.0% average divergence), resulting in the removal of 266 genes. The remaining 2,178 genes were examined for repetitive elements, short repeats, and low complexity regions, which are problematic for probe design and capture. The four sets of transcripts per gene (totaling 8,712 sequences) were screened using the REPEATMASKER Web Server (Smit et al. 2015). This step resulted in the masking of repetitive elements or low complexity regions in 929 sequences, with 7,783 sequences passing the filters. To be conservative, if any of the four transcripts for a gene contained masked sites, that gene was removed from the final marker set, which resulted in the removal of an additional 468 markers. From this reduced set of 1,710 markers, 400 markers with the highest divergence were selected (average divergence ranging from 10.4% to 14.9%) followed by 860 randomly drawn markers from the remaining subset. This marker set was supplemented with five positive controls, which consisted of nuclear sequence data generated using Sanger sequencing for five loci: POMC (624 bp), RAG-1 (777 bp), TYR (573 bp), FICD (524 bp), and KIAA2013 (540 bp). The final marker set selected for probe design included 1,265 genes from four species and 5,060 individual sequences.