7/27/2019 SDD1.101

1/7

SNPPEB 1.1

Software Design Document

(current document version 1.101)

Document update history:

version 1.0

Created by Tony on Aug 4, 2004

Description: First draft for general ideaversion 1.01

Modified by Tony on September 29, 2004

Draw flowchart to show design, and also address the issues in SRS1.01

Version 1.011Modified by Tony on Oct 1, 2004

Still address to SRS1.01More detailed module design in section 5.Version 1.012

Modified by Tony on Oct 6, 2004

Still address to SRS1.01Modify module design in section 5 from version 1.011.

Version 1.1

Modified by Tony on Jan 31, 2005Address to SRS 1.1

Major change:

1. provide service to new Backman GenomeLab SNPstream Genotyping System

2. Setup local databases instead of using XML files from NCBIVersion 1.101

Modified by Tony on Mar 10, 2005

Still address to SRS 1.1Redefine DB design

7/27/2019 SDD1.101

2/7

1. Description

The requirements in SRS will be fully addressed in this software design document or alternative

solution should be given. We will use reference sequence data from NCBI in fasta files and XML

file to setup our local dabases. Also, "Primer3"(http://frodo.wi.mit.edu/primer3/primer3_code.html) will be integrated into our application within

the useage condition in its copyright document.

2. Function Design

In this version of design document, we have a primary design to address the issues in SRS 1.1, anddraw a design flowchart.

a. Input and criteria

Input:

List of SNP ids

Two locations in a chromosome (Two STS markers?)Criteria:

Orientation: Original, all forward, all reverse

SNP types: (any combination)

6 types

Exclude coding SNPs?

Flanking sequence length?

Number of SNPs to be separated

Prototype is available at: http://bioinfo.vipbg.vcu.edu/SNPPEB/prototypes/

7/27/2019 SDD1.101

3/7

b. Query local databases

Database name: snppeb

i. ER:

ii. Table and column definition:

Table genome_contig:accession: accession.version format, example: NT_077402.1ctg_id: internal ID, example: CONTIG:77451tax_id: 9606 is Homo sapiensctg_length: length of contigchr: chromosome. Un is not placed on any chromosomechr_from: chromosome coordinate, reported in 1 base coordinates, starts

from 1. 0 means not localized or placed on any chromosomechr_to: chromosome coordinate, reported in 1 base coordinates. 0 means

not localized or placed on any chromosomeorient: +, -, 0, where 0 indicates uncertainty in orientationassembly: this value is used to associate contigs with a particular

assembly (e.g., reference assembly vs alternate assembliesprovided by other groups or representing other haplotypes)

Table genome_contig_set:

accession: accession.version format, example: NT_077402.1

7/27/2019 SDD1.101

4/7

segment_id: this is associated with ctg_from and ctg_to.Let ctg_from m ctg_toSegment_id = int((m-1)/200 + 1);

#ctg_from: contig coordinate, reported in 1 base coordinates, starts from1. Not added in DB, can be calculated from seqment_id:ctg_from = 200 * (segment_id 1);

#ctg_to: contig coordinate, reported in 1 base coordinates.

Not put in db.Can be calculated from segment_id and seq:ctg_to = 200 * (segment_id 1) + seq.length 1;

seq: sequence segment from contig, lower case means repetitive

Table snp_info:

id: rs#tax_id: species id, 9606 for humanbuild_create: build to create this SNPbuild_update: last build to update this SNPallele_1, allele_2: nucleotides in SNP site, 1 and 2 are in alphabet order

(example: A C, not C A)allele_1_frq: average frequency of allele_1

allele_2_frq: average frequency of allele_2frq_count: number of all chromosomes contributing to frequencycalculation.

validated_pop: T|F, at least one ss in cluster was validated by independentassay

validated_frq: T|F, at least one subsnp in cluster has frequency datasubmitted

validated_clu: T|F, cluster has 2+ submissions, with 1+ submission assayedwith a non-computational method

validated_2h2: T|F, all alleles have been observed in 2+ chrosomesvalidated_hap: T|F, validated by HapMap projectctg_accession: mapping contig in accession.version format, example:

NT_077402.1ctg_chr: chromosome of mapping contigctg_loc: snp location mapped to contig

chr_loc: snp location mapped to chromosomectg_ori: orientation of snp and flanking sequence to contigctg_fxn: functional relationship of SNP to genes at contig location:

locus-region |coding |conding-synon |coding-nonsynon | mrna-utr |intron |splice-site |reference |exception

Table snp_flanking:

id: rs#side: 5|3, 5 or 3 sidefragment: number index of fragment of a flanking sequence in order

5 side starts from the far end to SNP site, 3side startsfrom the immediate neighboring site of SNP

seq: fragement of flanking sequence

7/27/2019 SDD1.101

5/7

c. Information retrieval

SNP Information displayed:

Checkbox for further primer design

SNP id

Allele

Allele frequencies Flanking sequences, length and orientation

Verification information

function class(coding nonsynon, coding synon, ...)

location info (chr, contig, ...)

Prototype is available at: http://bioinfo.vipbg.vcu.edu/SNPPEB/prototypes/

d. Primer designi. Generate text file for autoprimer.com

ii. Primer in batch (call primer3)

Parameter setup

This page will be similar to the primer3 web application to setup parameters to run

primer3. The default value will be given according to suggestions from our lab

specialists.

Display Result

This page will display the primers for a list of SNPs. The format will be customized

by our lab specialists.

7/27/2019 SDD1.101

6/7

3. Flowchart

7/27/2019 SDD1.101

7/7

4. System Requirement and Running Enviroment

Programming tool: Java, PHP, Perl, CGI, BioPerl, XML::Twig

Primer design software: Primer3

Running environment: Redhat Enterprise Linux ws3, Dell workstation Precision 670

Database server: MySQLServer: bioinfo.vipbg.vcu.edu/SNPPEB

Client: IE, Mozilla, or Netscape browser and internet connection