6255 Gene Alignments Of Asellidae Cds

Families of orthologous genes used in "<strong>No evidence that nitrogen limitation influences the elemental composition of isopod transcriptomes and proteomes"</strong> The 6,255 alignments used in this publication are archived here. Each alignment corresponds to one "pattern" (~ gene family, except when one family X is composed of several patterns = e.g. multigenic family). Each alignment includes between 2 and 26 species. These alignments have been created with: prank -codon -F GBlocks -b5=h (to allow some gaps) Alignment are named according to the corresponding family_pattern, e.g. "FAM003424_1.fas.prank_codon.best.fas-gb.bis" corresponds to the family "003424" and the pattern "1". They are composed of several fasta sequences, each sequence corresponding to one species. The name of each fasta sequence starts with the species code (e: BMOV, PCANC) in upper letters. Gaps are present ("----"). ATTENTION: species order differs in each alignment! Table of the correspondance species - code: Species Code couple eco<br> P. beticus PBTS c1 epi<br> P. jaloniacus PJJ c1 hypo<br> P. aragonensis PARE c2 epi<br> P. spelaeus PSSE c2 hypo<br> B. peltatus BPM c3 epi<br> B. molinai BMOV c3 hypo<br> P. ibericus PIBB c4 epi<br> P. arthrodilus PATL c4 hypo<br> P. meridianus PMLL c5 epi<br> P. margalefi PMAF c5 hypo<br> P. granandensis PGRP c6 epi<br> P. solanasi PSOG c6 hypo<br> P. coxalis PCOB c7 epi<br> P. parvulus PPRS c7 hypo<br> P. assaforensis PASA c8 epi<br> P. rectus PRUE c8 hypo<br> P. karamani PKK c9 epi<br> P. hercegovinensis PHEZ c9 hypo<br> P. coiffaiti PCOIP c10 epi<br> P. cavaticus PCBF c10 hypo<br> P. racovitzai PRBE c11 epi<br> P. escolai PECD c11 hypo<br> P. ortizi POJ c12 epi<br> P. grafi PGC c12 hypo<br> P. ebrensis PEF c13 epi<br> P. cantabricus PCANC c13 hypo Remark: out of these 6,255 alignments, 8 alignments are empty (when Gblock has removed ALL aligned positions): [1] "FAM000157_5.fas" "FAM000587_3.fas" "FAM000615_1.fas" "FAM008836_1.fas" [5] "FAM013862_1.fas" "FAM015586_1.fas" "FAM017544_1.fas" "FAM022381_1.fas"本数据集使用的直系同源基因（orthologous genes）家族源自论文《氮限制对等足类动物转录组（transcriptome）与蛋白质组（proteome）的元素组成无影响》。 本研究使用的6255条比对文件已存档于此。每条比对对应一个“模式”（近似等同于基因家族，若某家族X包含多个模式时除外，例如多基因家族）。每条比对涵盖2至26个物种。上述比对通过以下流程构建： prank -codon -F GBlocks -b5=h（允许引入部分空位） 比对文件以对应的family_pattern命名，例如"FAM003424_1.fas.prank_codon.best.fas-gb.bis"对应家族"003424"与模式"1"。每个比对由多条FASTA（FASTA）序列组成，每条序列对应一个物种。每条FASTA序列的名称均以大写的物种代码（例如BMOV、PCANC）开头。序列中存在空位，以"----"表示。注意：每条比对中的物种顺序均不相同！ ### 物种-代码对应表： | 物种 | 代码 | 分组 | 生态型 | | ---- | ---- | ---- | ---- | | P. beticus | PBTS | c1 | epi | | P. jaloniacus | PJJ | c1 | hypo | | P. aragonensis | PARE | c2 | epi | | P. spelaeus | PSSE | c2 | hypo | | B. peltatus | BPM | c3 | epi | | B. molinai | BMOV | c3 | hypo | | P. ibericus | PIBB | c4 | epi | | P. arthrodilus | PATL | c4 | hypo | | P. meridianus | PMLL | c5 | epi | | P. margalefi | PMAF | c5 | hypo | | P. granandensis | PGRP | c6 | epi | | P. solanasi | PSOG | c6 | hypo | | P. coxalis | PCOB | c7 | epi | | P. parvulus | PPRS | c7 | hypo | | P. assaforensis | PASA | c8 | epi | | P. rectus | PRUE | c8 | hypo | | P. karamani | PKK | c9 | epi | | P. hercegovinensis | PHEZ | c9 | hypo | | P. coiffaiti | PCOIP | c10 | epi | | P. cavaticus | PCBF | c10 | hypo | | P. racovitzai | PRBE | c11 | epi | | P. escolai | PECD | c11 | hypo | | P. ortizi | POJ | c12 | epi | | P. grafi | PGC | c12 | hypo | | P. ebrensis | PEF | c13 | epi | | P. cantabricus | PCANC | c13 | hypo | 备注：在这6255条比对文件中，有8条为空比对（即GBlocks移除了所有比对位点），分别为： "FAM000157_5.fas"、"FAM000587_3.fas"、"FAM000615_1.fas"、"FAM008836_1.fas"、"FAM013862_1.fas"、"FAM015586_1.fas"、"FAM017544_1.fas"、"FAM022381_1.fas