Hi all,

I made BLASTp analysis on a specific genome against large databases. Here is my command line for example:

    > blastp -query SEQUENCE.fasta -db database -out blast_results -outfmt 6 -evalue 0.01 -max_target_seqs 5

As expected, my output files are very large and I would like to **select only the matches with a percentage of identical matches of 60 or higher**. 

Here is an example of an output file with only the first few lines:

    Prokka_00003	VFDB_prot_DB_VFG012837(gi:82524546)_(ipaH2.5)_invasion_plasmid_antigen,_fragment_[Mxi-Spa_TTSS_effectors_controlled_by_MxiE_(CVF465)]_[Shigella_dysenteriae_Sd197]	28.947	114	77	3	134	247	342	451	7.17e-05	44.7
    Prokka_00007	VFDB_prot_DB_VFG042740(gi:15599489)_(pprA)_two-component_sensor_PprA_[type_IV_pili_(AI098)]_[Pseudomonas_aeruginosa_PAO1]	29.496	278	175	5	463	735	654	915	8.18e-20	94.7
    Prokka_00007	VFDB_prot_DB_VFG038759(gb|YP_857329)_(fleS/flrB)_two-component_sensor_kinase_[ND_(AI144)]_[Aeromonas_hydrophila_subsp._hydrophila_ATCC_7966]	24.194	372	224	11	366	734	17	333	4.81e-19	89.4
    Prokka_00007	VFDB_prot_DB_VFG038760(gb|YP_008044159)_(flrB)_flagellar-related_two-component_sensor_kinase_[Polar_flagella_(VF0473)]_[Aeromonas_hydrophila_ML09-119]	24.194	372	224	11	366	734	17	333	6.71e-19	89.0
    Prokka_00007	VFDB_prot_DB_VFG038762(gi:330830289)_(flrB)_two_component_system_flagellar_sensor_histidine_kinase_FlrB_[Polar_flagella_(CVF786)]_[Aeromonas_veronii_B565]	26.141	241	163	5	497	734	105	333	7.11e-18	85.9
    Prokka_00007	VFDB_prot_DB_VFG038761(gi:145298503)_(flrB)_two-component_system_flagellar_sensor_histidine_kinase_FlrB_[Polar_flagella_(CVF786)]_[Aeromonas_salmonicida_subsp._salmonicida_A449]	25.311	241	165	5	497	734	105	333	1.28e-17	85.1

Do you know how would I be able to do that? 

Thank you so much for your much appreciated help!!

Have a nice day

According to the blast documentation, percent-identity is given in the third column of the standard output format "6". So you can simply sort or filter by the third column. In your example, there is no entry that satisfies your threshold.

    awk -F "\t"  '{if ($3 >=60) print $0}' blast-output.txt

Something like the above might work.