- General information
- Browser Incompatabilities
- BLAST methods
- PMN Datasets
- Entering query sequences
- Input file size limits
- Input data formats
- Filtering
- Result 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
- Click on Browse button
- Click on folders to open them, and on the file to upload it
- PC
- Click on the Browse button
- Change the file type from “HTML” to “all files”
- Click on folders to open them, and on the file to upload it
- UNIX
- Click on the Browse button
- Change *.html to * at the end of the string in the Filter box
- Click on a folder and then the Filter button to open the folder
- 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
Max Scores | |
| Restricts the number of short descriptions of matching sequences reported to the number specified; default limit is 25 descriptions. See also Expectation. | |
Max Alignments | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| 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 | |
| Penalty for a mismatch in the BLAST™ portion of run. | |
Nucleic Match | |
| Reward for a match in the BLAST™ portion of run. | |
Word Size | |
| The size of the initial word that must be matched between the database and the query sequence. | |
Matrix | |
| 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. | |
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 | 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 | 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 evident 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.