在序列类似性检索方面已开发研制了多种不同的应用软件,如BLAST、FASTA、Ssearch等,其中BLAST是最常用的检索软件之一。国内的科研人员大多凭经验利用BLAST进行序列类似性检索,未对其检索方法进行全面系统的研究,这极大地限制了BLAST的应用。卜西一一一目的:比较BLAST四种检索程序以及不同水平不同E值的检出量、查全率和...
No difference currently exists between the nucleotide alphabets used by AB-BLASTand WU-BLAST or the ability of programs in either package to search/modify nucleotide sequence databases created/modified by programs in the other package. The bundledBLOSUM30andBLOSUM35scoring matrices have been re-scaled...
After dereplication, users should give a careful check ofsizeof dereplicated FASTA files. It is worth noting that if a FASTA file with a very low amount of sequences, getting processed together with all the rest, the final "core" clusters will be heavily affected and may bias your analysis...
additional genome file to activate one-vs-all comparison, performing a local execution and using Docker nextflow run hoelzer/pocp -r 2.3.4 --genomes $HOME'/.nextflow/assets/hoelzer/pocp/example/*.fasta' --genome $HOME/.nextflow/assets/hoelzer/pocp/example/Cav_10DC88.fasta -profile local,...
but the query has to remain in plain fasta format. Another way to produce pairwise alignments with mmseqs would use the “search” function instead of easy-search. The search function requires databases built for both, query and target. The results of the search function is also in database...
Step 2 FASTA dereplication Step 2 is to remove potential sequence duplication (e.g., copies of tRNA, some cds). This dereplication is equivalent to 100% clustering, to obtain single copy. Step 2requires the tab separated table output by Step 1 as input, and specifying a directory for dere...