makeblastdb -in ST.pep.fa -dbtype prot -title ST.pep.fa
blastp -query AT.pep.fa -db ST.pep.fa -out ST_AT.blast -evalue 1e-10 -num_threads 16 -outfmt 6 -num_alignments 5
/biosoft/MCScanX/MCScanX/MCScanX ST_AT
得到以下结果
Reading BLAST file and pre-processing
Generating BLAST list
170 matches imported (1 discarded)
44 pairwise comparisons
0 alignments generated
Pairwise collinear blocks written to ST_AT.collinearity [0.013 seconds elapsed]
Writing multiple syntenic blocks to HTML files
AT1.html
AT2.html
AT3.html
AT4.html
AT5.html
ST1.html
ST10.html
ST11.html
ST12.html
ST2.html
ST3.html
ST4.html
ST5.html
ST6.html
ST8.html
Done! [0.172 seconds elapsed]
下面是ST_AT.collinearity 的结果
############### Parameters ###############
# MATCH_SCORE: 50
# MATCH_SIZE: 5
# GAP_PENALTY: -1
# OVERLAP_WINDOW: 5
# E_VALUE: 1e-05
# MAX GAPS: 25
############### Statistics ###############
# Number of collinear genes: 0, Percentage: 0.00
# Number of all genes: 55
##########################################
ST_AT.collinearity (END)
