• 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

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BLAST Methods

The NCBI BLAST family of programs hosted the PMN includes:

PMN BLAST Datasets

Entering query sequences

Multiple query sequences

Using the Browse option to upload a local file

• 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

Input file size limits

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

Result Formats:

Advanced parameters

File output options

Advanced options for Comma- and Tab-delimited formats

EXAMPLES

BLAST Options and Defaults

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

* Note: 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.