RNAalifold output from alignments of constrained regions in H1N1pdm09 viruses originating from human hosts, as predicted by RNAdescent.

Filename convention within the zip file is as follows: HA/NA type, then host type, then whether the region was identified through analysis of raw (unranked) data, ranked data, or both, then the gene name, then the nucleotide location within the analysed alignment of the gene name, then the nucleotide location within the reference sequences (corresponding to locations listed in S2 Table and S10 Table), then a note if the analysis was performed using only one example of each distinct sequence, then a note if the fold uses the reverse complement of the cRNA (i.e. the vRNA), rather than the cRNA. All folds have been generated using alignments with loci where the consensus nucleotide is a gap removed. Base pairs are highlighted in deep/mid/light red when all/all but one/all but two sequences are capable of forming the pairs shown. Base pairs are highlighted in deep/mid/light yellow when all/all but one/all but two sequences are capable of forming the pair shown or one other pair (including GU pairs). Base pairs are highlighted in deep/mid/light green when all/all but one/all but two sequences are capable of forming the pair shown or one of two other pairs (including GU pairs). RNAalifold was used with input options disallowing lonely pairs, allowing G-quadruplexes, and with the ribosum scoring matrix enabled.
(ZIP)

压缩包内的文件命名规范如下：文件名依次包含HA/NA型别、宿主型别、该区域的鉴定依据（原始未分级数据、分级数据或二者结合）、基因名称、该基因经比对分析后的核苷酸位点、参考序列中的核苷酸位点（对应S2表与S10表中所列位点）、若分析仅使用每条独特序列的单拷贝则添加的备注、若RNA二级结构折叠所使用的序列为互补RNA（cRNA）的反向互补链（即病毒RNA vRNA）而非cRNA本身，则添加相应备注。所有RNA二级结构折叠均基于移除了比对中共有核苷酸为缺口的位点后的序列比对生成。当全部、仅缺一条、仅缺两条序列均可形成图示碱基对时，分别以深、中、浅红色标记该碱基对。当全部、仅缺一条、仅缺两条序列均可形成图示碱基对或另一类碱基对（包括GU配对）时，分别以深、中、浅黄色标记该碱基对。当全部、仅缺一条、仅缺两条序列均可形成图示碱基对或另外两类碱基对之一（包括GU配对）时，分别以深、中、浅绿色标记该碱基对。本次分析采用RNAalifold工具（RNAalifold），输入参数设置为不允许孤立碱基对、允许G-四链体（G-quadruplexes）结构，并启用ribosum评分矩阵（ribosum scoring matrix）。（ZIP）