Selected databases are provided in CRISPRTarget. The database updates are provided in the news. 

In general Databases will be updated after each release of Genbank (even months) or RefSeq (odd months). The nt and env databases come from the BLAST databases and will be updated monthly.

Genbank (BLAST Nucleotide) databases, these are held locally but updated bimonthly with GenBank or RefSeq releases.

Databases are updated with full releases of Genbank and RefSeq (Note: Files (e.g. RefSeq plasmid.1.1.genomic.fna.gz. or GenBank gbphg1.seq.gz) files are downloaded, converted to fasta if needed, concatenated, converted to blast databases, and BLAST+ run locally)

• a) The nr/nt collection (~43 billion bases Genbank. This database contains "All GenBank + EMBL + DDBJ + PDB sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences)." (no longer availble due to size).
• b) env_nt. This contains "Sequences from environmental samples, such as uncultured bacterial samples isolated from soil or marine samples. The largest single source is Sargasso Sea project. This does not overlap with nucleotide nr". This is part of the whole genome shotgun (wgs) but these sequences have no taxonomic classification other than metagenome.
• c) Phage division (phg)

RefSeq databases: Several relevant divisions of the NCBI Reference Sequence databases are available, which contains better annotated (by NCBI) versions of GenBank sequences. Downloaded and updated evry two months here
• a) RefSeq-Plasmid.
• b) RefSeq-Viral.
• c) RefSeq-Archaea
• d) RefSeq-Bacteria (no longer availble due to size).

CAMERA database: We included viral parts of the CAMERA databases. 913,9883 gene sequences, 1 Billion bases (Files: CAM_PROJ_ReclaimedWaterVirues.read.fa, CAM_PROJ_MarineVirome.read.fa, CAM_P_0000909.read.fa, CAM_P_0000792.read.fa). ACLAME. 125,190 sequences, 96 million bases (V0.04, 8/2009, last version).

IMG/VR database: IMG_VR: IMGVR_all_nucleotides.fna.gz .  The current version is v4 Sept 2022 (or 6.1). IMG_VR_2022-09-20_6.1 - IMG/VR v4 - high-confidence genomes only (~80Gb). First version provided from 7/2018, legacy version in in the test directory 43 Gb  Oct 2020 v3 or 5.1 

This includes IMGVR viral contigs with IDS like IMGVR_UViG_2579779064_000006|2579779064|2579849396|1-17041, some genomes from RefSeq with IDs like NC_027986.1, and other entries Gammaproteobacteria_gi_553770258, and UGV-GENOME-3293712.

To interpret the results you will need the information file downloaded from here (requires JGI registration): IMG_VR: IMGVR_all_Sequence_information.tsv

HUVirDB Database downloaded from here : HuVirDB Assemblies opengut.ucsf.edu/HuVirDB-1.0.fasta.gz Cite Soto-Perez et al., 2019, Cell Host & Microbe 26, 325–335 https://doi.org/10.1016/j.chom.2019.08.008

User database: Users can upload sequences of up to 50 Mb (if you wish to analyse larger databases please contact us).

	The default values used by NCBI BLASTn for short sequences <30 bases (defaults for long sequences are in brackets) are:

			Gap open -5(-5)
			Gap extend -2(-2) 
			Match +1(+1)
			Mismatch -3(-3) 
			Word size 7(11) 
			Expect (E): 1000 (10)
			Filter: No (Yes)

Blastn-short (noticed 8/2018) now uses +2/-3 more similar to +1/-1 used here. A 30 base exact matrch is 60 for blastn-short and 30 for CRISPRTarget	
		
	The initial CRISPRTarget defaults are the same except that a gap is penalised more highly (-10), the mismatch penalty is -1 and the E filter is 1. 
	In addition, there is also no filter or masking for low complexity. BLAST calculates the scores over the length of the match, and only shows this 
	match. For example, a spacer of 32 bases that matches to a target in 	17 of 20 bases would score 20-3=17 and 20 bases would be output. The 
	expected (E) values of the match will be more likely to pass the filter if smaller databases are used (e.g. the default phg and plasmid).
	

	Changing BLAST parameters: Please note that only certain combinations of parameters produce valid statistics (this others will not work).
			For +1, -1 an attempt to use some combinations might fail. See the following example for allowed paramters:


		$ blastn -db database -query myseq -gapopen 1 -gapextend 1 -reward 1 -penalty -1

			BLAST engine error: Error: Gap existence and extension values 1 and 1 are not supported for substitution scores 1 and -1

				3 and 2 are supported existence and extension values

				2 and 2 are supported existence and extension values

				1 and 2 are supported existence and extension values

				0 and 2 are supported existence and extension values

				4 and 1 are supported existence and extension values

				3 and 1 are supported existence and extension values

				2 and 1 are supported existence and extension values

				4 and 2 are supported existence and extension values

				Any values more stringent than 4 and 2 are supported (e.g. 10, 2)
				
	Suggestion: Useful changes might be: 
	
			a. Reducing the gap penalty to 4 or 5 if you have reason to believe that gaps are tolerated in your system.

			b. Increasing the E to 10 or 100 in the unlikely event you are not getting hits.

			c. Increasing the mismatch penalty to -3 screens out mismatches.	

6. Set the DB size (effective database size). 
This is optional. This should be the total size of the databases you search. 

BLAST calculates the E (Expect) value based on the size of the database searched. 
If one search against multiple databases is done the database need not be specified as BLAST does it internally. 

To compare the significance of matches in two or more consecutive searches of different databases, 
this value should be set as the sum of the two databases sizes (e.g. for 270 Mb + 80 Mb= 350 Mb enter '350000000'). 

	5' crRNA handle length : The default value used is 8, but user can increase/decrease the length of the handle ranging from 0 to any number 
	(e.g: 100). There is no upper limit/restriction, but if the source sequence is not available, the length will be automatically adjusted. The 
	handle sequence belongs to the repeat sequences (unless the handle length is greater than repeat sequence length). 

	Score for each base match and mismatch : The default value set to 0, but user can alter the values to any positive or negative number
	(e.g: match: -1, mismatch: +1). If handle is present, these values can greatly help identifying the self matches. As, for self matches, the handle
	sequence of spacer will found all base pairing nucleotides. penalizing base pairing in the handle region will send the self matches down the order 
	or even filter them out (using the cutoff score).  
	
	Select PAM from the list : PAM (Protospacer Adjacent Motif) is often the key indicator of true positive CRISPR target match. It can be used to
	identify the targets of known CRISPR systems. The PAM types are shown below:
		I-A:	NGG
		I-B: 	NGG
		I-E:	CAT,CTT,CCT,CTC 
		I-C:	GAA 
		I-F:	GG
		
	Give PAM : User can also give a PAM motif (e.g: CGT). CRISPRTarget supports user given PAM to have IUPAC code. The following nucleotide codes 
	are supported.
	
			IUPAC_code	Base
				A	Adenine
				C	Cytosine
				G	Guanine
				T/U	Thymine (or Uracil)
				R	A or G
				Y	C or T
				S	G or C
				W	A or T
				K	G or T
				M	A or C
				B	C or G or T
				D	A or G or T
				H	A or C or T
				V	A or C or G
				N	any base
				./-	gap
		
	
	PAM match score: The default value is +5, but can use any positive or negative integer value. PAM score can greatly help reordering the output 
	and bring the true positive or target matches high in order. A combination of Spacer match/mismatch score, handle match/mismatch score and PAM 
	match score along with cutoff score can greatly improve the outcome, specially when the output consists of several hundreds of matches.     
	
	Seed require complementarity in the leading bases: This is one of the most important feature to directly filter out unsuitable matches 
	from the output. As BLAST report may contain hits with partial match between spacer and protospacer. Often it doesn't start from the first base
	of the spacer, but for many CRISPR systems it's a must that the leading bases (adjacent to the PAM) should not have any mismatch, or a mismatch
	might be allowed (e.g: 5th base) but not to the other leading bases (e.g: no mismatch to the first 1 to 4, and 6 to 8). Researchers with such 
	known models (properties), can apply the condition right at the very begining. For the said example, the input should be given as below:
			
			"Seed require complementarity in the leading 1-8 bases except base 5 of the spacer and protospacer pair."
	
	Note: if you want to exclude multiple bases, then give them comma separated. For the above example, if you want to exclude base 3 and 5, then 
	give input as below:
		
			"Seed require complementarity in the leading 1-8 bases except base 3,5 of the spacer and protospacer pair."		
	

	3' crRNA handle length : The default value used is 8, but user can increase/decrease the length of the handle ranging from 0 to any number 
	(e.g: 100). There is no upper limit/restriction, but if the source sequence is not available, the length will be automatically adjusted. The 
	handle sequence belongs to the repeat sequences (unless the handle length is greater than repeat sequence length). 

	Score for each base match and mismatch : The default value set to 0, but user can alter the values to any positive or negative number
	(e.g: match: -1, mismatch: +1). If handle is present, these values can greatly help identifying the self matches. As, for self matches, the handle
	sequence of spacer will found all base pairing nucleotides. penalizing base pairing in the handle region will send the self matches down the order 
	or even filter them out (using the cutoff score).  
	
	Select PAM from the list : PAM (Protospacer Adjacent Motif) is often the key indicator of true positive CRISPR target match. It can be used to
	identify the targets of known CRISPR systems. The PAM types are shown below:
		
		II-A:	WTTCTNN,TTTYRNNN 
		II-B:	CNCCN,CCN

		
	Give PAM : User can also give a PAM motif (e.g: CGT). CRISPRTarget supports user given PAM to have IUPAC code. The following nucleotide codes 
	are supported.
	
			IUPAC_code	Base
				A	Adenine
				C	Cytosine
				G	Guanine
				T/U	Thymine (or Uracil)
				R	A or G
				Y	C or T
				S	G or C
				W	A or T
				K	G or T
				M	A or C
				B	C or G or T
				D	A or G or T
				H	A or C or T
				V	A or C or G
				N	any base
				./-	gap
		
	
	PAM match score: The default value is +5, but can use any positive or negative integer value. PAM score can greatly help reordering the output 
	and bring the true positive or target matches high in order. A combination of Spacer match/mismatch score, handle match/mismatch score and PAM 
	match score along with cutoff score can greatly improve the outcome, specially when the output consists of several hundreds of matches.     
	
	Seed require complementarity in the leading bases: This is one of the most important feature to directly filter out unsuitable matches 
	from the output. As BLAST report may contain hits with partial match between spacer and protospacer. Often it doesn't start from the first base
	of the spacer, but for many CRISPR systems it's a must that the leading bases (adjacent to the PAM) should not have any mismatch, or a mismatch
	might be allowed (e.g: 5th base) but not to the other leading bases (e.g: no mismatch to the first 1 to 4, and 6 to 8). Researchers with such 
	known models (properties), can apply the condition right at the very begining. For the said example, the input should be given as below:
			
			"Seed requires complementarity in the leading 1-8 bases except base 5 of the spacer and protospacer pair."
	
	Note: if you want to exclude multiple bases, then give them comma separated. For the above example, if you want to exclude base 3 and 5, then 
	give input as below:
		
			"Seed requires complementarity in the leading 1-8 bases except base 3,5 of the spacer and protospacer pair."