Name: NCBI Online BLAST
Author: Scott Markel
Version: 2.0
Created: 02/2005
Modified: 08/2007 (This Readme text)
Purpose: Run Blast on-line on the NCBI server

Descriuption:  These component runs blastall online at NCBI to generate BLAST results that are added to the sequence data record. A hit list data record is output for each input query sequence. The hits can be extracted from the hit list for individual
manipulation using the Extract BLAST Hits component. Sequences with no BLAST hits are routed to the fail port. There are parameters for the database name and for the expectation value.

blastn compares incoming nucleotide sequences with a nucleotide database, resulting in nucleotide alignments.

blastp compares incoming protein sequences with a protein database, resulting in protein alignments.

blastx compares incoming nucleotide sequences with a protein database, resulting in protein alignments.

tblastn compares incoming protein sequences with a nucleotide database, resulting in protein alignments.

tblastx compares incoming nucleotide sequences with a nucleotide database, resulting in protein alignments.

The NCBI Online BLASTn component supports the following nucleotide databases:
- nr  All GenBank+RefSeq Nucleotides+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences). No longer "non-redundant"
- est  Database of GenBank+EMBL+DDBJ sequences from EST Divisions
- est_human  Human subset of GenBank+EMBL+DDBJ sequences from EST Divisions
- est_mouse  Mouse subset of GenBank+EMBL+DDBJ sequences from EST Divisions
- est_others  Non-Mouse, non-Human sequences of GenBank+EMBL+DDBJ sequences from EST Divisions
- gss  Genome Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences
- htgs  Unfinished High Throughput Genomic Sequences: phases 0, 1 and 2 (finished, phase 3 HTG sequences are in nr)
- pat  Nucleotides from the Patent division of GenBank
- pdb  Sequences derived from the 3-dimensional structure from Brookhaven Protein Data Bank
- month  All new or revised GenBank+EMBL+DDBJ+PDB sequences released in the last 30 days
- alu  Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences
- dbsts  Database of GenBank+EMBL+DDBJ sequences from STS Divisions
- chromosome  Searches Complete Genomes, Complete Chromosome, or contigs form the NCBI Reference Sequence project

Requirements: Pipeline Pilot 6.1.1
O/S: PP Server Windows and Linux
PP client Windows
Limitations: None
Keywords: NCBI, blast, DNA, RNA, Protein, alignment
Contents: Components:
NCBI Online BLASTn.xml
NCBI Online BLASTp.xml
NCBI Online BLASTx.xml
NCBI Online tBLASTn.xml
NCBI Online tBLASTx.xml

Installation: Drag and drop the components on the component area.