BatchPrimer3 | Tool name | BatchPrimer3 |
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| URL | http://probes.pw.usda.gov/cgi-bin/batchprimer3/batchprimer3.cgi |
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| Important features | 1. Allows the user to input multiple set of sequences. It will take maximum of 500 sequences at a time to process.
2. It has the primer parameters similar to primer 3.
3. Designs several types of primers including generic primers for any DNA sequences, hybridization oligos, SSR primers together with SSR detection, and SNP genotyping primers (including single-base extension primers, allele-specific primers, and tetra-primers for tetra-primer ARMS PCR), as well as DNA sequencing primers.
4. Mis-priming library is available for plants only. |
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| Citations | You FM, Huo N, Gu YQ, Luo MC, Ma Y, Hane D, Lazo GR, Dvorak J, Anderson OD. BatchPrimer3: a high throughput web application for PCR and sequencing primer design. BMC Bioinformatics. 2008 May 29;9:253. PubMed PMID: 18510760. |
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| Year of publication | 2008 |
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| Rank by usage frequency | 100 |
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| Comments | Very fast working tool. |
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| Function | Sequencing primers, SNP primers, Allele specific primers, Masking the repeat sequence, Predicting secondary structure |
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| Category | Online, Free |
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| Features | 1. A batch input of large number of sequences and a tab-delimited result output greatly facilitates rapid primer design and ordering process.
2. Online results can be saved in different formats.
3. Multiple sequences can be given as an input, has an option to perform a pre-analysis of input sequence, and tool returns sequence length, GC%, ambiguity code etc. |
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| Description | For,
1) amplification of same gene from different organism
2) microbial ecology study by designing primer based on protein sequence. |
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