SNP_Primer_Pipeline怎么用
SNP_Primer_Pipeline怎么用
这篇文章主要介绍了SNP_Primer_Pipeline怎么用的相关知识，内容详细易懂，操作简单快捷，具有一定借鉴价值，相信大家阅读完这篇SNP_Primer_Pipeline怎么用文章都会有所收获，下面我们一起来看看吧。
之前在做dcaps标记，开始只找到网站版的软件，后来发现一个不错的脚本软件——SNP_Primer_Pipeline
利用其中的 getCAPS-with-user-input.py 可以同时做caps和dcaps标记引物设计，用法如下：
pythongetCAPS-with-user-input.py-iinput.fa-tchr5D:9950377_Ref-p301-rA-aC-m1000
其中 -i:输入序列；-t: 目标序列；-p: SNP位置；-r: ref；-a: alt；-m: 价格上限。
输入文件：
>chr5D:9950377_RefTATCCATGCACATTAACATAGAAAAATTAAGTATAGAGGGTTGTCATGTATATACCGGAAAGAAGCTCCTCAAGGGTTCCACCCTGCATGTATTCCAAACATAGAGCTATTTCTTGCTCGTCAGCAACAACAAATCTCCCTTGGTACTCAACAACTTTATCTCGTATTTCATAGCAGTAGCCAACCAATCTTATGATATTTTGATGTTGGGCCCTCATAAGATTCAGAAGCTCATTCTTAAAACCAGCTTCGACTAGTCCGGGCTGGTTGTACAGTTTCTTCACGGCAATCACTTCCCCGTTATCAAGTACTCCCTGTTCAAAATCCCATGTTTAAAAGTAATAATGCAAGGGTTCAGGTAGCTAGTGTAGTGGTGGCATCTGTTTAAAAGTATTATTTTTTTCGTAAAATGCGCTTAATTTTCCTCCCAGCAACCTTTCCACCAACTGATGCACATATAACTTTGCGGTTGTAAAGTAGAAGATACAAGTAAATAATCATACTTCACACAAAAGCCTTAGAAACTACTCCCTATCCACCACAAACAATTATACGCTGCTTACAAAAATTAACGGGAGAGGAAATTACTGCCTTGGTGCTG
输出结果：
indexproduct_sizetypestartenddiff_number3'differalllengthTmGCcontentany3'end_stabilityhairpinprimer_seqReverseComplementpenaltycompl_anycompl_endPrimerIDmatched_chromosomesSNP-dCAPS-Hpy166II,68-gtnnac-303-0193LEFT1351560YES2258.68545.4550.00.03.160.0tctcccttggtactcaacaactagttgttgagtaccaagggaga8.8497234.482.64L1SNP-dCAPS-Hpy166II,68-gtnnac-303-0193RIGHT3273030YES2559.46540.010.4910.492.830.0ggattttgaacagggagtacttgTtaAcaagtactccctgttcaaaatcc8.8497234.482.64R1SNP-dCAPS-BsrBI,66-ccgctc-302-0192LEFT1351560YES2258.68545.4550.00.03.160.0tctcccttggtactcaacaactagttgttgagtaccaagggaga9.5459044.4810.00L1SNP-dCAPS-BsrBI,66-ccgctc-302-0192RIGHT3263020YES2558.76940.00.00.03.270.0gattttgaacagggagtacttgaGatCtcaagtactccctgttcaaaatc9.5459044.4810.00R6SNP-dCAPS-BsrI,63-ccagt-300-0161LEFT2813000YES2060.32255.00.00.04.450.0tcacggcaatcacttcccAgcTgggaagtgattgccgtga0.43397613.9613.96L3SNP-dCAPS-BsrI,63-ccagt-300-0161RIGHT4414220YES2059.88855.00.00.03.360.0ggaaaggttgctgggaggaattcctcccagcaacctttcc0.43397613.9613.96R2SNP-dCAPS-HpyCH4IV,132-acgt-299-0163LEFT2792990YES2159.80252.3810.00.04.020.0cttcacggcaatcacttccAcgTggaagtgattgccgtgaag1.31013317.9712.50L9SNP-dCAPS-HpyCH4IV,132-acgt-299-0163RIGHT4414220YES2059.88855.00.00.03.360.0ggaaaggttgctgggaggaattcctcccagcaacctttcc1.31013317.9712.50R2SNP-dCAPS-Fnu4HI,330-gcngc-298-0163LEFT2792980YES2060.17955.00.00.04.70.0cttcacggcaatcacttcGcgCgaagtgattgccgtgaag0.2916276.814.00L8SNP-dCAPS-Fnu4HI,330-gcngc-298-0163RIGHT4414220YES2059.88855.00.00.03.360.0ggaaaggttgctgggaggaattcctcccagcaacctttcc0.2916276.814.00R2SitesthatcandifferallforSNPCAPScutinformationforsnpSNPEnzymeEnzyme_seqChange_posOther_cut_posCac8I,710gcnngc295BseYI,660cccagc298427HhaI,HinP1I,29gcgc297412PsiI,560ttataa304HpaI,122gttaac303CviKI-1,272rgcy298361,229,262,514,105,210,179,246,64Hpy166II,68gtnnac303
关于“SNP_Primer_Pipeline怎么用”这篇文章的内容就介绍到这里，感谢各位的阅读！相信大家对“SNP_Primer_Pipeline怎么用”知识都有一定的了解，大家如果还想学习更多知识，欢迎关注恰卡编程网行业资讯频道。
