Oly Blast 1 using refseq_protein database¶

In [1]:

!blastx -query /Volumes/web/scaphapoda/Hannah/Olurida_transcriptome_v3.fasta -db /Volumes/web/whale/blast/db/refseq_protein -out /Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_refseq_protein.txt -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 10

Oly Blast 1 Modified¶

!tr '|' "\t" /Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_1_mod.txt

Oly Blast 7 using est_others database¶

In [24]:

!blastn -query /Volumes/web/scaphapoda/Hannah/Olurida_transcriptome_v3.fasta -db /Volumes/web/whale/blast/db/est_others -out /Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_7.txt -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 12

shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
BLAST Database error: No alias or index file found for nucleotide database [/Volumes/web/whale/blast/db/est_others] in search path [::]

Oly Blast 7 Modified¶

In [1]:

!tr '|' "\t" </Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_7.txt> /Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_7_mod.txt

In [2]:

!head /Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_7_mod.txt

comp339_c0_seq1	gi	313369999	gb	HS233142.1		89.72	107	11	0	7	113	42	148	2e-29	 137
comp1381_c0_seq1	gi	51568059	gb	CV088710.1		82.61	69	12	0	129	197	115	183	1e-06	62.1
comp1447_c1_seq1	gi	164578412	emb	AM858910.1		86.36	198	20	6	2	193	292	96	7e-51	 209
comp1570_c0_seq1	gi	152817395	gb	EH647498.1		90.91	99	8	1	138	235	278	180	1e-27	 132
comp1594_c0_seq1	gi	313314075	gb	HS170088.1		86.24	109	12	2	1	107	513	406	1e-22	 115
comp2352_c0_seq1	gi	372694305	gb	HO350921.1		89.58	240	19	5	5	241	1270	1506	3e-78	 300
comp4323_c0_seq1	gi	168496333	emb	CU683729.1		86.87	99	13	0	123	221	49	147	1e-21	 111
comp5108_c0_seq1	gi	291574798	gb	GR484415.1		89.39	66	7	0	86	151	68	3	3e-13	84.2
comp6696_c0_seq1	gi	313318047	gb	HS177103.1		88.82	161	18	0	4	164	1	161	1e-47	 198
comp6696_c0_seq2	gi	313318047	gb	HS177103.1		88.82	161	18	0	4	164	1	161	4e-47	 198

Oly Blast 6 using nt database¶

!blastn -query /Volumes/web/scaphapoda/Hannah/Olurida_transcriptome_v3.fasta -db /Volumes/web/whale/blast/db/nt -out /Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_6.txt -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 7

Oly Blast 6 Modified¶

!tr '|' "\t"

Oly Blast 11 using env_nt database¶

In [19]:

!blastn -query /Volumes/web/scaphapoda/Hannah/Olurida_transcriptome_v3.fasta -db /Volumes/web/whale/blast/db/env_nt -out /Volumes/web/scaphapoda/Hannah/Blast/Oly_Blast_env_nt.txt -outfmt 6 -evalue 1E-5 -max_target_seqs 1 -num_threads 8

shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
BLAST Database error: No alias or index file found for nucleotide database [/Volumes/web/whale/blast/db/env_nt] in search path [::]

Oly Blast 11 Modified¶

In []: