TcSNP Guide

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Website Sections:

In the Genes page you can search for genes/sequences:
  • using parameters like gene name, GenBank accession, keywords, Gene Ontology (GO) terms
  • from a specific strain
  • by properties of the multiple-sequence alignment containing that sequence: alignment ID, number of SNPs, number of aligned sequences, dN/dS ratio.

NOTE: Each search field (i.e. each parameter that you enter) is processed independently. It means that the only processed parameter is the one at the left of the "search" button clicked. If you want to combine different parameters (e.g. alignments with more than 10 SNPs containing a sequence from strain Tul2) go to HISTORY section.

Once you enter an argument and click Search, you will access a list of genes/sequences that matched, where you can see some basic information about those genes (e.g. description, accession, strain, # of SNPs ) and follow a link to the alignment that contains each gene.
In the SNPs page you can find specific polymorphic sites searching by:
  • SNP ID (unique numeric code that we assigned to each snp)
  • the alignment where the SNP is obvserved (by TcSNP unique AlignmentID)
  • SNP score, a measure of the probability of the polimorphism to be true (ranging from 0 to 1)
  • the location in a region with high density of SNPs (defined as more than 3 SNPs within a 10-bases window)
  • the capacity of the polymorphism on discriminating between two strains (very useful for identifying SNPs for typifying strains/stocks/isolates)
  • the efect of the SNP on the coded aminoacid (synonymous, non-synonymous, non-sense)

NOTE: Each search field (i.e. each parameter that you enter) is processed independently. It means that the only processed parameter is the one at the left of the "search" button clicked. If you want to combine different parameters (e.g. polymorphism between CL-Brener and strain CanIII AND Non Synonymous mutation AND score > 0.5) go to HISTORY section.

Once you enter an argument and click Search, you will access a list of SNPs that matched, where you can see some basic information about them (e.g. SNP ID, Score, Position in Alignment ) and follow a link to the alignment that contains each SNP.

HISTORY Page
Where you can examine the queries that you have run, and construct more complex queries combining query sets using operators UNION, INTERSECTION, and SUBSTRACTION. ... ... ...