max_hsps_1_dict[bn.qseqid][bn.sseqid] = bnelse: max_hsps_1_dict[bn.qseqid] = {bn.sseqid: bn}# 第一步:检查normal.txt去重完成后是否只剩244行了normal_cnt =0forqseqidinnormal_dict: normal_cnt +=len(normal_dict[qseqid])print('去除query ID和subject ID完全相同的行后,%s还剩下%s...
1)-num_alignments 2)-max_target_seqs 3)-num_descriptions 4)-max_hsps 这个4个命令有时容易搞混,在使用时每个都一次就可以区分,这里ChatGPT讲的还是比较详解。 3. 控制输出的格式(默认是-outfmt 6) 输出结果直接影响着我们如何看比对结果。 这里是一个blastn的输出结果一共12列,看一下每一列代表着什么?
[-max_hsps int_value] [-xdrop_ungap float_value] [-xdrop_gap float_value] [-xdrop_gap_final float_value] [-searchsp int_value] [-penalty penalty] [-reward reward] [-no_greedy] [-min_raw_gapped_score int_value] [-template_type type] [-template_length int_value] [-dust DUST_...
It is possible for what should be a single HSP to look like multiple HSPs if the extension terminates (low sequence quality and hard-masking cause this). True splicing events are easily identified from their coordinates; there ought to be a large coordinate gap in the genome but not the ...
ext.args = '--evalue 1e-5 --max-hsps 1 --max-target-seqs 200 -b 6 --outfmt 6' To investigate: It looks like DIAMOND can build the database with taxon info and limit to 1 hit per species, which is more ideal. e.g. build... (note this has been done and the taxon_mapped...
BLASTN参数研究记之max_hsps 最近频繁使用到BLASTN,BLASTN有很多参数。有一些显而易见的参数,例如: -query -out -outfmt -db 也有一些参数不那么常用,今天主要研究研究这些不常用的参数。 1. 准备数据 主要用的数据有: BLASTN索引文件 Query序列 假定这些文件都放置在当前文件夹,并且当前文件夹有一个ret的子文...