down_genome_refseq.pl txid9606 > human_refseq.faThus, to look at human (txid9606), mouse (txid10090), rat (txid10116), and pig (txid9823), you would run the command:
down_genome_refseq.pl txid9606 > human_refseq.fa down_genome_refseq.pl txid10090 > mouse_refseq.fa down_genome_refseq.pl txid10116 > rat_refseq.fa down_genome_refseq.pl txid9823 > pig_refseq.faTo convert these to searchable blast protein databases:
makeblastdb -in human_refseq.fa -out human_refseq -title human_refseq -parse_seqids -taxid 9606 -dbtype prot makeblastdb -in mouse_refseq.fa -out mouse_refseq -title mouse_refseq -parse_seqids -taxid 10090 -dbtype prot makeblastdb -in rat_refseq.fa -out rat_refseq -title rat_refseq -parse_seqids -taxid 10116 -dbtype prot makeblastdb -in pig_refseq.fa -out pig_refseq -title pig_refseq -parse_seqids -taxid 9823 -dbtype prot
A script designed to compare/contrast the set of hits produced by searching against a different set of sequence databases (typically different genomes). The script assumes:
blastp -outfmt 7 -query my_queries.lib -db human_refseq > myq_v_human.bp blastp -outfmt 7 -query my_queries.lib -db mouse_refseq > myq_v_mouse.bp blastp -outfmt 7 -query my_queries.lib -db rat_refseq > myq_v_rat.bp summ_blasttab_hits.pl myq_human.bp myq_mouse.bp myq_rat.bp > myqueries.summaryProduces a file with each query in the first field, and then a summary of the hits from the first file in the 2 - 7, the second file in 8 - 13, etc:
# col:1 2 3 4 5 6 7 # query best hit acc best #hits worst eval percid eval percid # prot_v_human.bp prot_v_mouse.bp sp|P69905|HBA_HUMAN ref|NP_000508.1| 2e-99 100.00 18 2e-08 27.52 ref|NP_001077424.1| 8e-87 86.62 21 1e-04 25.50 sp|P00502|GSTA1_RAT ref|NP_665683.1| 6e-124 76.13 23 0.001 30.00 ref|NP_032207.3| 3e-154 94.57 49 6e-06 24.11 sp|P01593|KV101_HUMAN ref|XP_006725506.1| 1e-44 80.00 9 0.001 26.27 ref|XP_006544145.1| 2e-21 54.08 14 7e-05 31.52 sp|P99998|CYC_PANTR ref|NP_061820.1| 1e-72 100.00 1 1e-72 100.00 ref|NP_031834.1| 4e-66 91.43 3 8e-61 83.65 sp|P60615|NXL1A_BUNMU sp|P02585|TNNC2_HUMAN ref|NP_003270.1| 2e-110 100.00 296 0.001 23.33 ref|NP_033420.1| 1e-108 98.75 346 0.001 24.39 sp|P00193|FER_PEPAS ref|XP_005274072.1| 0.001 33.93 1 0.001 33.93 ref|NP_659119.2| 0.001 33.93 3 0.001 33.93The summary columns report the best hit accession, evalue, and percent identity, and the worst (significant) evalue and percent identity, repeating for the next file.