PMN BLAST 2.2.8

• General information
• Browser Incompatabilities
• BLAST methods
• PMN Datasets
• Entering query sequences
• Input file size limits
• Input data formats
• Filtering
• Results options
• Advanced parameters
• File output options

General Information

BLAST stands for Basic Local Alignment Search Tool and was developed by Altschul et al. (1990) and significantly improved by Altschul et al. (1997). It is a very fast search algorithm that is used to separately search protein or DNA databases. BLAST is best used for sequence similarity searching, rather than for motif searching. For searches using a query sequence of fewer than twenty residues, other programs, such as PatMatch for Arabidopsis thaliana proteins at TAIR. To search additional datasets, you may try NCBI BLAST. 
A fairly complete on-line guide to BLAST searching can be found at the NCBI BLAST Help Manual. For a theoretical overview of BLAST, see the NCBI BLAST Course. Additional information can be found in the BLAST 2.0 Release Notes

Browser Incompatibilities

Note: This site has been tested with IE8.X, Safari 3.X and Firefox/Mozilla 5.X browsers. Some pages may not work as expected if you are using older browsers.

BLAST Methods

The NCBI BLAST family of programs hosted the PMN includes:

blastp:
	compares an amino acid query sequence against a protein sequence database.
blastx
	compares a nucleotide query sequence translated in all reading frames against a protein sequence database.

 

PMN BLAST Datasets

The following datasets are available for PMN-BLAST-2.2.8 
 

Dataset	Type	Description	Source
Reference Enzymes (3.1)	Protein	Reference Enzymes from RPSD 3.1 (2015). Enzymes with experimentally supported*activity and protein sequence information. Includes enzymes from all kingdoms and some enzymes not directly involved in metabolism.	UniProt-KB/SwissProt (2015), BRENDA (2015), MetaCyc 18.5, and PlantCyc 9.5
PlantCyc Enzymes	Protein	Enzymes found in PlantCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	PlantCyc 10.0 (June 2015)
AraCyc Enzymes	Protein	Enzymes found in AraCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	AraCyc 13.0 (June 2015)
BarleyCyc Enzymes	Protein	Enzymes found in BarleyCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	BarleyCyc 3.0 (June 2015)
BrachypodiumCyc Enzymes	Protein	Enzymes found in BrachypodiumCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	BrachypodiumCyc 3.0 (June 2015)
CassavaCyc Enzymes	Protein	Enzymes found in CassavaCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	CassavaCyc 5.0 (June 2015)
ChineseCabbageCyc Enzymes	Protein	Enzymes found in ChineseCabbageCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	ChineseCabbageCyc 3.0 (June 2015)
ChlamyCyc Enzymes	Protein	Enzymes found in ChlamyCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	ChlamyCyc 5.0 (June 2015)
CornCyc Enzymes	Protein	Enzymes found in CornCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	CornCyc 6.0 (June 2015)
GrapeCyc Enzymes	Protein	Enzymes found in GrapeCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	GrapeCyc 5.0 (June 2015)
MossCyc Enzymes	Protein	Enzymes found in MossCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	MossCyc 4.0 (June 2015)
OryzaCyc Enzymes	Protein	Enzymes found in OryzaCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	OryzaCyc 3.0 (June 2015)
PapayaCyc Enzymes	Protein	Enzymes found in PapayaCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	PapayaCyc 4.0 (June 2015)
PoplarCyc Enzymes	Protein	Enzymes found in PoplarCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	PoplarCyc 8.0 (June 2015)
PotatoCyc Enzymes	Protein	Enzymes found in PotatoCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	PotatoCyc 2.0 (June 2015)
SelaginellaCyc Enzymes	Protein	Enzymes found in SelaginellaCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	SelaginellaCyc 4.0 (June 2015)
SetariaCyc Enzymes	Protein	Enzymes found in SetariaCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	SetariaCyc 3.0 (June 2015)
SorghumBicolorCyc Enzymes	Protein	Enzymes found in SorghumBicolorCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	SorghumBiColorCyc 3.0 (June 2015)
SoyCyc Enzymes	Protein	Enzymes found in SoyCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	SoyCyc 6.0 (June 2015)
SpirodelaCyc Enzymes	Protein	Enzymes found in SpirodelaCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	SpirodelaCyc 1.0 (June 2015)
SwitchgrassCyc Enzymes	Protein	Enzymes found in SwitchgrassCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	SwitchgrassCyc 3.0 (June 2015)
TomatoCyc Enzymes	Protein	Enzymes found in TomatoCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	TomatoCyc 1.0 (June 2015)
WheatACyc Enzymes	Protein	Enzymes found in WheatACyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	WheatACyc 1.0 (June 2015)
WheatDCyc Enzymes	Protein	Enzymes found in WheatDCyc with known protein sequences. Both experimentally and computationally supported enzymes are included.	WheatDCyc 1.0 (June 2015)
Reference Enzymes (3.0)	Protein	Reference Enzymes from RPSD 2.0 (2012). Enzymes with experimentally supported*activity and protein sequence information. Includes enzymes from all kingdoms and some enzymes not directly involved in metabolism.	SwissProt 15.3, BRENDA, and MetaCyc
Reference Enzymes (2.0)	Protein	Reference Enzymes from RPSD 1.0 (2011). Enzymes with experimentally supported*activity and protein sequence information. Includes enzymes from all kingdoms and some enzymes not directly involved in metabolism.	SwissProt 15.3
Reference Enzymes (1.0)	Protein	Reference Enzymes from RESD 1.0 (2009). Enzymes with experimentally supported*activity and protein sequence information. Includes enzymes from all kingdoms and some enzymes not directly involved in metabolism.	UniProt (2009), MetaCyc (12.5), BRENDA (2009), TAIR8

Entering query sequences

When pasting sequences into the text box, be aware that a single sequence is limited to 7000 characters in length; when you paste multiple sequences (up to five are allowed) you are limited to a total of 15,000 characters. These limitations may be changed in the future. If you have a longer sequence, or many sequences, use the file upload feature. This feature is not supported on some versions of Microsoft's Internet Explorer web browser. If you do not see a "Browse..." button near the file upload text box (that displays your computer's filesystem directory when clicked), we suggest using Netscape or another browser supporting file uploading.

Multiple query sequences

To submit multiple query sequences, paste up to 5 sequences into the input box or,upload a file containing the concatenated sequences in FASTA format. For this option the files cannot be in raw format because they will be interpereted as a single query sequence. For NCBI-BLAST it may be possible to upload more than five sequences depending on the length of the query sequence and size of the target database.See the following section on Input file size limits. WuBLAST has a defined limit of 5 sequences.

Using the Browse option to upload a local file

NOTE:If you are uploading a file, make sure the file is in text format. If your file is a WORD document, open the file in Word and save again as text only format.

• Macintosh

1. Click on Browse button
2. Click on folders to open them, and on the file to upload it

• PC

1. Click on the Browse button
2. Change the file type from "HTML" to "all files"
3. Click on folders to open them, and on the file to upload it

• UNIX

1. Click on the Browse button
2. Change *.html to * at the end of the string in the Filter box
3. Click on a folder and then the Filter button to open the folder
4. Click on a file and then the OK button to upload it

Word documents will not work unless saved as text first.

Input file size limits

For NCBI BLAST limits are imposed on the size of the input files based upon the type of query being performed and the size of the dataset being searched. For example, the limit for TBLASTX against a large data set such as GenBank AGI sequences is 1000 characters, whereas for a small dataset like TIGR CDS sequences the limit is 3000 characters. The following table lists the search type and limits for NCBI Blast. If your files are larger, try using WU-BLAST2 instead. 
 

Search Type	Large data set input character limit	Small data set input character limit
BLASTN	25000	25000
BLASTX	25000	25000
BLASTP	5000	5000
TBLASTN	1000	3000
TBLASTX	1000	3000

Input Data Formats

• Raw text format

  An example sequence in raw format is:

  GGAAAAATCGAAGGATAATCTGTTTCTTCCAGCACAAGTTAACTTGCAAGAGAGAGCT
  CAAAGATGGAACCAACAGAAAAACCATCGACCAAACCATCTTCTCGGACTCTACCTAG
  AGACACTCGTGGCTCTCTCGAAGTATTCAACCCGTCAACTCAGCTGACCCGACCCGAT
  AACCCGGTGTTCCGTCCTGAACCACCAGCGTGGCAAAACTTGAGTGATCCACGTGGCA
  CCAGTCCTCAACCCCGACCACAACAAGAACCAGCTCCATCCAACCCTGTTCGGTCTGA
  TCAAGAAATCGCTGTCACGACCTCATGGATGGCTCTGAAAGACCCATCACCGGAGACA
  ATCTCCAAG
  

• FASTA format

  A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. It is recommended that all lines of text be shorter than 80 characters in length. An example sequence in FASTA format is:

  >gi|1122533|gb|AAB05099.1| BELL1
  MARDQFYGHNNHHHQEQQHQMINQIQGFDETNQNPTDHHHYNHQIFGSNSNMGMMIDFSKQQQIRMTSGS
  DHHHHHHQTSGGTDQNQLLEDSSSAMRLCNVNNDFPSEVNDERPPQRPSQGLSLSLSSSNPTSISLQSFE
  LRPQQQQQGYSGNKSTQHQNLQHTQMMMMMMNSHHQNNNNNNHQHHNHHQFQIGSSKYLSPAQELLSEFC
  SLGVKESDEEVMMMKHKKKQKGKQQEEWDTSHHSNNDQHDQSATTSSKKHVPPLHSLEFMELQKRKAKLL
  SMLEELKRRYGHYREQMRVAAAAFEAAVGLGGAEIYTALASRAMSRHFRCLKDGLVGQIQATSQALGERE
  EDNRAVSIAARGETPRLRLLDQALRQQKSYRQMTLVDAHPWRPQRGLPERAVTTLRAWLFEHFLHPYPSD
  VDKHILARQTGLSRSQVSNWFINARVRLWKPMIEEMYCEETRSEQMEITNPMMIDTKPDPDQLIRVEPES
  LSSIVTNPTSKSGHNSTHGTMSLGSTFDFSLYGNQAVTYAGEGGPRGDVSLTLGLQRNDGNGGVSLALSP
  VTAQGGQLFYGRDHIEEGPVQYSASMLDDDQVQNLPYRNLMGAQLLHDIV
  

• GCG format

  An example sequence in GCG format is:

  !!NA_SEQUENCE 1.0
  nga361
  nga361.seq  Length: 204  February 22, 1999 12:09  Type: N  Check: 234  ..
  1  TTATATGATA TATATAGTTA TGTATGTTNC AAGAATNCGA TATGGNACGC
  51  ATGATTGAAG AATAATGATT GAGGAATTTT NCTGTAACAA AAAAATTNGA
  101  NATAAACAAN TNTGTGGCTA AGAACTTAAC AAGGNCACAT GTTGATATGT
  151  GAANTAGGAA TCTCATNATA AGGANCACAC GGTTGACAGC AAACGGGCNT
  201  NTAC
  

• RSF format

  A Rich Sequence Format (RSF) file contains one or more sequences that may or may not be related. In addition to the sequence data, each sequence can be richly annotated with descriptive sequence information such as creator/author of the sequence, sequence weight, creation date, one-line description of the sequence, offset, or the number of leading gaps in a sequence that is part of an alignment or fragment assembly project, and known sequence features. An example sequence in RSF format is:

  !!RICH_SEQUENCE 1.0
  ..
  {
  name  Hs70_Plafa
  descrip    PileUp of: @Hsp70.List
  type    PROTEIN
  longname  Gendocdisk:[Gcgdoc.Program_Manual]Hsp70.Msf{Hs70_Plafa}
  checksum    1012
  creation-date 10/15/96  8:40:33
  strand  1
  sequence
  ~~~~~~~~~~~~~~~MASAKGSKPNLPESNIAIGIDLGTTYSCVGVWRNENVDIIANDQG
  NRTTPSYVAFT.DTERLIGDAAKNQVARNPENTVFDAKRLIGRKFTESSVQSDMKHWPFT
  VKSGVDEKPMIEVTYQGEKKLFHPEEISSMVLQKMKENAEAFLGKSIKNAVITVPAYFND
  SQRQATKDAGTIAGLNVMRIINEPTAAAIAYGLHKKG..KGEKNILIFDLGGGTFDVSLL
  TIED...G.IFEVKATAGDTHLGGEDFDNRLVNFCVEDFKRKNRGKDLSKNSRALRRLRT
  QCERAKRTLSSSTQATIEIDSLFEGID....YSVTVSRARFEELCIDYFRDTLIPVEKVL
  KDAMMDKKSVHEVVLVGGSTRIPKIQTLIKEFFNGKEACRSINPDEAVAYGAAVQAAILS
  G.DQSNAVQDLLLLDVCSLSLGLETAGGVMTKLIERNTTIPAKKSQIFTTYADNQPGVLI
  QVYEGERALTKDNNLLGKFHLDGIPPAPRKVPQIEVTFDIDANGILNVTAVEKSTGKQNH
  ITITNDKGRLSQDEIDRMVNDAEKYKAEDEENRKRIEARNSLENYCYGVKSSLEDQKIKE
  KLQPAEIETCMKTITTILEWLEKN.QLAGKDEYEAKQKEAESVCAPIMSKIYQDAAGAAG
  .GMPGGMP..GGMPGGMPSGMPGGMNFPGGMPGAGMPGNAPAGSGPTVEEVD~~~~~~
  }
  

Filtering

Filtering masks off segments of the query sequence that have low compositional complexity, as determined by the SEG program of Wootton & Federhen (Computers and Chemistry, 1993) or, for BLASTN, by the DUST program of Tatusov and Lipman (in preparation). Filtering can eliminate statistically significant but biologically uninteresting reports from the BLAST output (e.g., hits against common acidic-, basic- or proline-rich regions), leaving the more biologically interesting regions of the query sequence available for specific matching against database sequences.

Filtering is only applied to the query sequence (or its translation products), not to database sequences. Default filtering is DUST for BLASTN, SEG for other programs. It is not unusual for nothing at all to be masked by SEG, when applied to sequences in SWISS-PROT, so filtering should not be expected to always yield an effect. Furthermore, in some cases, sequences are masked in their entirety, indicating that the statistical significance of any matches reported against the unfiltered query sequence should be suspect.

Results Options

Output title
	Type in the title you would like to appear at the top of your BLAST output.
E-mail address:
	Entering your email address is suggested even if requesting a browser reply, and may be mandatory depending on server configuration options. Depending on server loading, or the expected execution time of your request, the server may convert your request to an email reply and auto-select the E-mail URL option. This avoids the frustration of wondering when your job will finish, and allows you to request more jobs quicker.

Return Results:

To your web browser
	Your job will run immediately and return results directly to your Web browser in HTML format. Accession numbers that appear in the query and target loci names and descriptions will be hyperlinked to allow easy access to additional sequence information.  NOTE: Attempting to view large result files may cause your browser to "blank out". If you have trouble viewing results, particularly if you've asked for many scores and alignments, or submitted many queries in one job, your browser's "memory" and "disk" cache settings may need to be increased. See your browser's help and preference menus for details. To prevent loss of a large HTML result file, you might wish to request emailing a URL to it rather than a browser reply. This way you'll be able to experiment with your browser's cache settings and retrieve the output as many times as you wish without waiting for your request to be re-run.
By E-mail message
	The results are sent within the body of a normal email message, to the email address you enter. Any comments you type will appear as the Subject of the email message. Generally, you should use this option only if your mail system can handle large messages, and you've asked for textual output. If requesting HTML format by email, either of the following choices may be better if your mail reader software is not HTML-aware.
By E-mail notice to URL
	Many mail systems have trouble with large email messages, and may split or truncate them. Our blast server will retain your results and send you a short email containing a URL (Uniform Resource Locator; to use with your web browser or HTML-aware mail reader) indicating where to obtain your results. We will delete your results after the date and time indicated in the email message.

Result Formats:

HTML hypertext (file type "htm")
	HTML format is used by web browsers. Accession numbers that appear in the query and target loci names and descriptions will be hyperlinked to allow easy access to additional sequence information. Embedded Java "Applets" may be used to render graphical information (e.g., the ClustalW dendrogram), which will not appear unless your browser is set to permit these applets to run.
Normal text (file type "txt")
	The results are returned as conventional human-readable text.
Comma-delimited records (file type "csv")
	Information is returned as quoted, comma-separated fields and records, compatible with Excel, Word, Access and most database products. These products allow simple viewing and sorting on any data column. For each query sequence, each rank score produces a record. Alignment text is included in those records when available. For example, if you ask for the best 100 scores and best 25 alignments, the alignment text fields will be null strings for the last 75 records of each query. For BLAST scores that return more than one alignment, a separate record is generated for each.
Tab-delimited records (file type "tab")
	Similar to comma-delimited, but no quotes are used, and tabs replace comma characters as the field separator. More commonly used in UNIX environments. The meaning of the columns are following.  DNA: RANK, STATUS, SCORES, E-VALUES, PROGRAM, Gap Penalties (Existence), Gap Penalty (Extension), empty, empty, MATRIX, TEMPFILENAME, QUERY LENGTH, Frame of Query that the score was found for (empty for protein), QUERY NAME, DATASET, Target length, Frame of Target that the score was found for (empty for protein), DESCRIPTION, empty, emtpy, empty, empty, empty, empty, empty, empty, empty, Identities, empty, Gaps, Percentage ratio of identical matches to the length of the alignment, Percentage ratio of identical matches to the length of the query, unknown, unknown, empty, empty, empty, Query Start, Query End, Target Start, Target End, QUERY NT, COMPARISON, TARGET NT  Protein: RANK, STATUS, SCORE, E-VALUE, PROGRAM, Gap Penalties (Existence), Gap Penalty (Extension), EMPTY, EMTPY, MATRIX, TEMPFILENAME, QUERY LENGTH, empty, QUERY NAME, DATASET, Target length, empty, DESCRIPTION, empty, empty, empty, empty, empty, empty, empty, empty, empty, Identities, Positives, Gaps, Percentage ratio of identical matches to the length of the alignment, Percentage ratio of identical matches to the length of the query, unknown, unknown, Percentage ratio of identical matches to the length of the target, unknown, unknown, Query Start, Query End, Target Start, Target End, empty, QUERY NT, COMPARISON, TARGET NT

Advanced parameters

View Default Settings

Max Scores Default Setting
	Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 25 descriptions. See also Expectation.
Max Alignments Default Setting
	Restricts database sequences to the number specified for which high-scoring segment pairs (HSPs) are reported; the default limit is 15. If more database sequences than this happen to satisfy the statistical significance threshold for reporting (see Expectation), only the matches ascribed the greatest statistical significance are reported.
Expectation Default Setting
	The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECTATION threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable.
Query and Database Genetic Code Default Setting
	Genetic code to be used in BLASTX translation of the query.
Gapped Alignments
	Whether to allow gapped alignments; either ON or OFF.
>Gap Opening Penalty Default Setting
	Cost to open a gap; a 0 in the field means to use the default. Supported values for BLASTP, BLASTX, TBLASTN, and TBLASTX are limited.
Gap Extension Penalty Default Setting
	Cost to extend a gap, a 0 in this field means to use the default. Supported values for BLASTP, BLASTX, TBLASTN, and TBLASTX are limited.
Nucleic Mismatch Default Setting
	Penalty for a mismatch in the BLAST™ portion of run.
Nucleic Match Default Setting
	Reward for a match in the BLAST™ portion of run.
Word Size Default Setting
	The size of the initial word that must be matched between the database and the query sequence.
Matrix Default Setting
	The amino acid substitution matrix to be used for protein comparisons. Both BLOSUM and PAM matrices are available at several different levels of evolutionary distance.
Extension Threshold
	The threshold above which BLAST™ will extend a hit found. The hit is based on finding a word of a certain size (see Word Size)
Reporting Threshold
	This keyword allows a score value to be specified as the threshold for displaying scores. Scores below this value are not shown.

File output options

Advanced options for Comma- and Tab-delimited formats

Header-Record if checked, the first record will contain the field names as shown in the table below.
Selected Fields if left blank, a default set of fields is returned. To customize, select from the following keywords; put a space between each. 

 

KEYWORDS

ClustalW does not presently support tab- and comma-delimited formats.
The fieldlist can contain any of the following keywords in any order and repeated as desired:

SEARCHID	Place the name of the search file in the record.
RANK	Place the score rank number in the record.
SCORE	Place the score in the record.
PSCORE	Place the p-score in the record.
ALGORITHM	Specify the algorithm to be used in the search.
ITERATION	Iteration number for PSIBLAST searches.
OPENPENALTY	Place the Open Penalty in the record.
EXTENDPENALTY	Place the Extend Penalty in the record.
FRAMEPENALTY	Place the Frame Penalty in the record.
SCALEFACTOR	Indicates the scale factor used. Default is 1.
MATRIX	Place the name of the PAM matrix file in the record.
QUERYNUMBER	Place the number of the query in the record. This number represents which query sequence the record is when multiple query files or multiple sequences are used in the search
QUERYFILE	Place the name of the query file in the record
QUERYLENGTH	Place the length of the query file in the record.
QUERYFRAME	Place the frame of the query with which the score was calculated, in the record.
QUERYTEXT	Place the description from the query file in the record.
TARGETFILE	Place the name of the target in which the score was found, in the record.
TARGETLENGTH	Place the length of the target locus in which the score was found, in the record.
TARGETFRAME	Place the frame of the target locus in which the score was found, in the record.
TARGETLOCUS	Place the name of the target locus in which the score was found, in the record.
TARGETACCESSION	Place the accession number of the target locus in which the score was found, in the record.
TARGETDESCRIPTION	Place the description of the target locus in which the score was found, in the record.
PERCENTSCORE	Place the ratio of the score to the maximum possible score in the record.
MAXSCORE MAXSCORED MAXSCOREC MAXSCORE1 MAXSCORE2 MAXSCORE3 MAXSCORE-1 MAXSCORE-2 MAXSCORE-3	Place the maximum possible score in the record. These fields may be empty if a search was not requested in the frame referenced in the field.
MATCHES	Place the total number of alignment character matches in the record. These are perfect matches.
SIMILARITIES	The number of identical and similar matches.
GAPS	Place the total number of alignment gaps in the record.
PERCENTALIGNMENT	Place the ratio of the total identical matches to the alignment length in the record.
PERCENTQUERY	Place the ratio of the total identical matches to the query length in the record.
PERCENTTARGET	Place the ratio of the total identical matches to the target locus length in the record.
SIMPERCENTALIGNMENT SIMPERCENTQUERY SIMPERCENTTARGET	These are the same as the percent fields above, except that the percentage is that of similar matches, not the identical matches.
QUERYSTART	Place the query start location in the record.
QUERYEND	Place the query end location in the record.
TARGETSTART	Place the target locus start location in the record.
TARGETEND	Place the target locus end location in the record.
QUERY	Place the query data for the alignment in the record.This field is for BLAST searches only. Use the following fields for Smith-Waterman related searches.
QUERYNT	Place the query nucleotide data for the alignment in the record.
QUERYAA	Place the query amino acid data for the alignment in the record.
COMPARISON	Place the alignment comparison information in the record.
TARGET	Place the target locus nucleotide data for the alignment in the record.This field is for BLAST searches only. Use the following fields for Smith-Waterman related searches.
TARGETNT	Place the target locus nucleotide data for the alignment in the record.
TARGETAA	Place the target locus amino acid data for the alignment in the record.

EXAMPLES

FIELDS: RANK SCORE QUERYNT COMPARISON TARGETNT

This example causes comma-delimited output to contain the specified fields. A sample output may look like the following:

"1", "10.0","ACGT","|| ", "ACAC"
"2", "5.0","ACGT","| ", "ATAC"

 

BLAST Options and Defaults

	BLASTP	BLASTX
Gap opening penalty:  cost to open a gap [integer]	default = 11 limited values are supported	default = 11 limited values are supported
Gap extension penalty:  cost to extend a gap [integer]	default = 1 a 0 in this field means to use the default	default = 1 a 0 in this field means to use the default
Nucleic match: reward for a match in the BLAST portion of run [integer]	n/a	n/a
Nucleic mismatch: penalty for a mismatch in the blast portion of run [integer]	n/a	n/a
Expectation value: (E) [real]	default = 10.0	default = 10.0
Word size: the size of the initial word that must be matched between the database and the query sequence	default = 3	default = 3
Max scores: Number of one-line descriptions (V) [Integer]	default = 25	default = 25
Max alignments: number of alignments to show (B) [integer]	default = 15	default = 15
Query filter: filter applied to the query sequence	default = SEG	default = SEG
Query genetic code: genetic code to be used in BLASTX translation of the query	n/a	default = universal
Matrix: substitution matrix to be used for amino acid comparisons	default = blosum62	default = blosum62

 

Supported and Suggested Values for Gap Open and Extension in BLASTP, BLASTX, TBLASTN, and TBLASTX

Gaps Open	Gap Extension
10	1
10	2
11	1
8	2
9	2

* Note: For Reference Enzymes 3.0 and above, an enzyme was considered to be experimentally supported if it had a 4-part EC and some evidence of expression in UniProt-KB/SwissProt, or if it had a publication associated with it in BRENDA, or if it had an experimentally evidence in MetaCyc 18.5 or PlantCyc 9.5. For Reference Enzymes 2.0, an enzyme in SwissProt that had a 4-part EC and some evidence of expression was considered to be experimentally supported. For Reference Enzymes 1.0, an enzyme was considered to be experimentally supported if it had a GO evidence code of IDA, IMP, IPI, IGI, or IEP in any of the data sources, or if it had a publication associated with it in BRENDA.