pero_in.454.fasta

This file contains 454 generated fastq reads for the Peromyscus samples used for the probe development. Both individuals included in the concatenated reference sequence are within this file, with USNM 569292 represented as 92. Sample USNM 569298 is represented as reads ID'd as 98

Enrichment Assemblies

These are all 63 assemblies, in bam format with the resulting consensus sequences as fasta. All sequences are labelled by capture pool ID in table 2

AllProbes_good

This file contains all 8,178 probes used for RNA bait synthesis

sequenceGetter-4.0

This script gets a subset of a FASTA file based on a CSV file of BLAST hits

WMG_Alignment26Ind_FINAL01.09.14

All mitochondrial genomes used for array design. 16 are published sequences and 10 are novel mitogenomes

H3FTPWM01

454 Sequencing reads for some of newly generated mitogenomes, a text file is provided with demultiplexing information and for this run

chimera_ID

This script sorts capture sequences that hit to non-closest-relative (NCR) MMA probes

combiner-2.0

The FASTA file is sequences from MMA capture. The Blast output is the output of blasting those sequences against the MMA probeset, minus closest relative to the target species (non-closest-relative, or NCR, probeset). This program appends the length of the query sequence (found in the FASTA file) onto the end of that sequence's line in the blast table so that the chimera detection decision rules can be followed in chimera_ID.p

Estimates of Tajima’s D^*.

<p>*The analysis involved 9 KoRV sequences. Codon positions included were 1st+2nd+3rd. All positions containing gaps or missing data were eliminated. There were 1565 positions for <i>gag</i>, 3384 for <i>pol</i>, 1980 for <i>env</i>, and 6929 positions for all (concatenated coding sequences) in the final dataset. Abbreviations: m  =  number of sequences; S = Number of segregating sites; ps = S/m; Θ = ps/a1; π = nucleotide diversity; D = Tajima test statistic.</p

The effects of historical KoRV polymorphisms on protein structure.

<p>Superimpositions are shown between the present day consensus KoRV (Pci-SN265) protein structure and ancient KoRV variants. Amino acid variations between these sequences mapped on the protein models are shown in red and with arrows. The models are shown in cartoon ribbon representations (left panels) and as semi-transparent surfaces (right panels). The atoms of the variable amino acid residues are in line representations to view the side chains. In all comparisons the Pci-SN265 consensus was used as the reference sequence. (A) The model of the Pci-SN265 Gag protein is superimposed with the models of variants found in archival koalas um3435 and maex1738. (B) The model of the Pci-SN265 Pol protein is superimposed with variants found in QMJ6480, 582119, MCZ8574, Um3435, and maex1738. (C) The model of the Pci-SN265 Env protein is superimposed with the model of variants found in MCZ_12454 and um3435. For all three polypeptides, the structural differences predicted are attributed to changes in the polarity, charge, and atom conformations and are largely localized onto flexible loop regions.</p