SNPbox | Tool name | SNPbox |
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| URL | http://www.snpbox.org/ |
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| Important features | |
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| Citations | Weckx S, De Rijk P, Van Broeckhoven C, Del-Favero J. SNPbox: a modular
software package for large-scale primer design. Bioinformatics. 2005 Feb
1;21(3):385-7. Epub 2004 Sep 3. PubMed PMID: 15347573. |
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| Year of publication | 2005 |
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| Rank by usage frequency | 100 |
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| Comments | Not yet identified the unique feature of the tool. Features are written as claimed by the author. Refer Feature Table for the detail description of the tool. |
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| Function | Sequencing primers, SNP primers, General PCR, Masking the repeat sequence, Predicting secondary structure |
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| Category | Online, Free, Free for academic |
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| Features | 1. Primer designing for SNP analysis.
2. SNP box holds 3 modules for automated primer design - a SNP module, an exon module and a saturation module.
a) The SNP module allows the user to design primers for the validation of public SNPs. Aligns target sequence to the hapmap SNP data to identify the presence of SNP's in the target. SNP's found within a region of 300 bp are joined into one object [block].
b) In the exon module - Identifies the exon region by aligning the gDNA [target] with cDNA or EST sequences. Also it checks for the presence of SNP using Hapmap data.
3. Allows the user to mask the repeat sequence.
4. Allows the user to select the chromosome in order to align with hapmap database. |
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| Description | |
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