I'm trying to run eggnog-mapper in a computing cluster that I've never used before have eggnog-mapper v2.1.10 stuck forever in the pfam annotation step. I've used v2.1.9 in another cluster with the same settings and had no issue with it. This is the .out file: # emapper-2.1....
Heger, AFinn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.-R., Ceric, G., Forslund, K., Eddy, S.R., Sonnhammer, E.L.L. and Bateman, A. (2008) The Pfam protein families database, Nucl. Acids Res., 36, D281-288....
Usage:pfam_scan.pl-fasta<fasta_file>-dir<directory location of Pfam files>Additonal options:-h:showthishelp-outfile<file>:output file,otherwise send to STDOUT-clan_overlap:show overlapping hits within clan member families(applies to Pfam-A families only)-align:show the HMM-sequence alignmentforea...
hmm 3.使用hmmscan 进行Pfam注释 Pfam 数据库中每个编号代表一个蛋白质家族。Pfam 分 A 和 B 两个数据库,其中 A 数据库是经过手工校正的高质量数据库, B 数据库虽然质量低些,依然可以用来寻找蛋白质家族的保守位点。Pfam 30.0以后的版本,Pfam-B就去除掉了,所以我们只关心PfamA就好了。 # 因为我要查看结构...
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EvoDB contains 98.83% of the gapped nucleotide sequence alignments and 97.1% of the evolutionary rate profiles for the corresponding information in PFAM-A. As the identification of codon sites under positive selection and their position in a sequence profile is usually the most sought after ...
L. Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB. Bioinformatics, v. 28, n. 21, p. 2763, 11, 2012.Xu Q and Dunbrack RL Jr. Assignment of pro- tein sequences to existing domain and family classification systems: Pfam and the PDB....