Introduction
The server presents SNPs found in putative coding regions of a specified focus species, based on DNA sequence alignments with a closely related reference species that is already assembled and annotated. SNP and SAP positions are listed for each coding exon in the requested gene, along with protein and/or DNA alignments of the exons. The following request will return all SNPs in the coding region of putative orthologous gene "SDK1" in species Tasmanian devil, along with sequence alignments of exons between orthologous genes in focus species and its close-related species, Opossum.
Currently, this website provides coding SNPs information in two species, Tasmanian devil, bighorn-sheep. A detailed description on how we annotated SNPs and how to use this website will be described below.
Focus species, reference species, and query gene names
"Focus species" is the species with SNPs information, like "Tasmanian devil" shown above. We predicted putative protein-coding orthologous regions and annotated SNPs in focus species by aligning focus species reference assembly with a close-related species with existing assembly and annotation information. Take "Tasmanian devil" for instance, we aligned reference Sarcophilus assembly with Opossum's monDom5 assembly. This close-related species, Opossum, is "reference species". Therefore, although "query gene names", which is input in the form for "Gene", should use gene name symbols in reference species, they are gene names of orthologous genes in focus species. As in the above, "SDK1" is the putative orthologous gene in Tasmanian devil. Species used as references for each focus species is in the following table:
SNP Annotation
Based on coding exons annotation in putative orthologous genes in focus species, SNPs in coding region were annotated as synonymous SNPs or nonsynonymous SNPs (SAPs). Putative protein-coding genes prediction in focus species was conducted by aligning focus species reference assembly with DNA sequences of Ensembl-annotated protein-coding exons in transcripts in reference species. The protein-coding exons sequences in reference species were downloaded from UCSC Genome Browser. We obtained partial set of exons with satisfied alignment (alignment with at least 75% identity and without an insertion or deletion). For those genes with unaligned or partial aligned exons, we cannot acquire complete protein sequences. Therefore, our SNP annotation is based on aligned coding exons in reference species and only for SNPs in coding region.How to use this website?
To pull out SNPs information in focus species, choose the focus species in the "Species" option list, type the query gene name (namely, gene name symbol in reference species) in "Gene" text field, and then click "Get SNP Info" button. Waiting for few seconds, the result will be shown in the bottom box.Input
The input for the query includes focus species,
, and query gene name, 
. focus species can be chosen from option list. I will describe query gene names in more details below.
As introduced in the "Focus species, reference species, and query gene names" part, gene names of putative orthologous gene in focus species should use gene name symbols in reference species. For different species, types of gene ID that can be accepted as gene name are different. The following table contains an example of allowed gene identifier for each species:
The input field of query gene name,
,is with autocomplete function. To activate autocomplete list, type three letters in the gene names (if the name is RefSeq DNA ID, please type five letters). A list of candidate gene names including these letters will pop up automatically and users can choose the corresponding gene from the list.
Setting parameters
Parameters are set for different layout of presentation of alignments. There are four parameters can be customized by users:- Show alignments as: whether to show only protein alignment or DNA alignment, or both protein alignment and DNA alignment in the result. Default value is "Protein".
- Number of characters in each line of alignment: choose how many letters are in each line of alignment. Default value is "50".
- Show matching bases/residues as: whether to use "dot" to represent identical bases/residues in alignment sequences. Default value is "dot".
- In the alignment sequences: Show all alleles in the focus species or show only one allele in the focus species: In alignment between reference species and focus species, in addition to variation in reference species and allele in focus species reference assembly, whether to show the other allele in focus species (if there is no SNP in that exon, this allele will be the same with the one in focus species reference assembly). Default value is "Show all alleles in the focus species".
Output
The output is shown in the table, by putative coding exons of orthologous genes in focus species. If there are more than one transcripts with aligned exons associated with this gene, corresponding numbers of tables will be in the output. Only exons that have satisfied alignment between reference species and focus species will be shown in the result. All SNPs in those exons, namely coding SNPs, in the putative orthologous gene will be presented. Below is the schema for the output table: