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R脚本在数据库/文学中的胰蛋白酶消化后找到肽

[英]R script to find peptides after trypsin digest in databases/literature

原文 2015-12-11 11:46:44 1 1 r/ automation/ sequence/ bioinformatics/ digest

I have a long list of peptide sequences which I would like to look up in batch mode in public sources/ databases, to see if the peptides have been identified as biomarkers in specific tissues (plasma, urine, etc). 我有一长串肽序列，我想在公共资源/数据库中以批处理模式查找这些肽序列，以查看是否已将这些肽鉴定为特定组织（血浆，尿液等）中的生物标记。 The problem is that the peptides have been generated using a trypsin digest, which means that I do not always get exact matches and need to also find inexact matches to my peptide queries by finding cases with irregular digest cleavages. 问题在于，这些肽段是使用胰蛋白酶消化生成的，这意味着我并不总是能获得完全匹配的结果，还需要通过查找具有不规则消化酶切片段的病例来寻找与我的肽段查询不精确的匹配项。 The only R packages I am finding that can handle issues with enzyme digests deal with spectra rather than peptide sequences. 我发现的唯一可以处理酶消化问题的R软件包处理的是光谱而不是肽序列。 I would appreciate any suggestions on how to do this, thanks! 我将不胜感激任何有关此操作的建议，谢谢！

1 个解决方案

I've used the "Cleaver" R package in the past, it seems to have the most comprehensive list of enzymes that I've come across yet: 我过去使用过“ Cleaver” R软件包，它似乎具有我所遇到的最全面的酶列表：

devtools::install_github("sgibb/cleaver") devtools :: install_github（ “sgibb /切割器”）

R重复调用后关闭变化的摘要 - R digest of closure changes after repeated call

在R中使用dplyr后，为什么data.frame的摘要会更改？ - Why is the digest of a data.frame changed after the use of dplyr in R?

R查询中的摘要功能 - Digest function in R query

R digest::digest() 不返回预期的哈希值 - R digest::digest() does not return expected hashes

发布到 Power BI 服务后出现 R 脚本运行时错误 - 找不到 function“label_number” - R-script runtime error after publishing to Power BI service - could not find function "label_number"

无法在R中下载“摘要”包 - Can not Download 'digest' package in R

在 R 中使用摘要身份验证的 POST 请求 - POST request with digest auth in R

R中的for循环和数据库 - For loop and databases in R

HMAC和R“摘要”包中的换行符出错 - Error with HMAC and newlines in R “digest” package

摘要 package 未安装在 R - lgfortran 未找到 - digest package not installing in R - lgfortran not found

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