Harvard:Biophysics 101/2007/Notebook:Resmi Charalel/2007-4-17: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
(New page: Applications: Our program can be used for a variety of applications. In particular, it is able to locate single nucleotide polymorphisms (SNPs) in an entered DNA sequence and return any...) |
No edit summary |
||
| Line 1: | Line 1: | ||
Applications | ==Applications== | ||
*Our program can be used for a variety of applications. In particular, it is able to locate single nucleotide polymorphisms (SNPs) in an entered DNA sequence and return any corresponding phenotypic correlations listed in Online Mendialian Inheritance in Man (OMIM). Using the disease correlation, the program will then print a paragraph of the phenotypes associated with the SNP and return a series of references of related peer-reviewed articles. Currently, it is possible to enter a given disease-correlated SNP and return information about the disease itself and the risk of the individual whose sequence was entered to the disease. In the future, with the rise of personal genomics and more expansive databases containing sequence information, such an application will become more useful. | |||
How to Use Our Program | ==How to Use Our Program== | ||
*Enter a sequence of interest into our web interface in a fasta format and click “GO” (subject to change). The program will then compare your sequence against all known sequences in NCBI BLAST and return an rs number for each unique SNP found. Along with the rs number and SNP, details including any known phenotypic associations and relevant references are printed in a paragraph derived from OMIM. These references as well as review article references from PubMed are also returned for further reading on the subject. | |||
How Our Program Works | ==How Our Program Works== | ||
*Our program is written in Python, a programming language, which allows access to NCBI BLASTsnp, PubMed, and OMIM as well as other biologically relevant databases through BioPython. Our program is designed to enter the given sequence into BLASTsnp and parse the resulting XML output to retrieve all rs numbers of any known SNPs in the sequence, which correspond to those in the database. This rs numbers are then entered into OMIM to search for any phenotypic relevance of the SNP and all returned entries are parsed to return the allelic variant name, mutation and description (including relevant references). The rs number and allelic variant name are then entered into NCBI PubMed and references specific to the allelic variant and the general phenotypic result are returned for further reading. | |||
Latest revision as of 21:07, 16 April 2007
Applications
- Our program can be used for a variety of applications. In particular, it is able to locate single nucleotide polymorphisms (SNPs) in an entered DNA sequence and return any corresponding phenotypic correlations listed in Online Mendialian Inheritance in Man (OMIM). Using the disease correlation, the program will then print a paragraph of the phenotypes associated with the SNP and return a series of references of related peer-reviewed articles. Currently, it is possible to enter a given disease-correlated SNP and return information about the disease itself and the risk of the individual whose sequence was entered to the disease. In the future, with the rise of personal genomics and more expansive databases containing sequence information, such an application will become more useful.
How to Use Our Program
- Enter a sequence of interest into our web interface in a fasta format and click “GO” (subject to change). The program will then compare your sequence against all known sequences in NCBI BLAST and return an rs number for each unique SNP found. Along with the rs number and SNP, details including any known phenotypic associations and relevant references are printed in a paragraph derived from OMIM. These references as well as review article references from PubMed are also returned for further reading on the subject.
How Our Program Works
- Our program is written in Python, a programming language, which allows access to NCBI BLASTsnp, PubMed, and OMIM as well as other biologically relevant databases through BioPython. Our program is designed to enter the given sequence into BLASTsnp and parse the resulting XML output to retrieve all rs numbers of any known SNPs in the sequence, which correspond to those in the database. This rs numbers are then entered into OMIM to search for any phenotypic relevance of the SNP and all returned entries are parsed to return the allelic variant name, mutation and description (including relevant references). The rs number and allelic variant name are then entered into NCBI PubMed and references specific to the allelic variant and the general phenotypic result are returned for further reading.
