Remote Query plugin

This plugin provides capability to annotate sequences with information stored in remote databases.
The result of the query is stored as a set of annotations to the sequence.

To implement remote database search open DNA sequence view, select the sequence region to analyse and click "Analyse->Query remote database" item from the context menu. If region is not selected full-size sequence will be sought.

In following dialog you can choose search options:

Select Search
You can use blastn for nucleotide sequences, blastp and cdd for amino sequences. Also you can search nucleotide sequence with blastp and cdd, UGENE will automatically convert the sequence into 6 possible translations using translation table from the active sequence view.
Expect value
This setting specifies the statistical significance threshold for reporting matches against database sequences. Lower expect thresholds are more stringent, leading to fewer chance matches being reported.
Max hits
Maximum number of hits, that will be shown (not equal to number of annotations).
Database
Target database.
Search for short sequences
Automatically adjust word size and other parameters to improve results for short queries.
Megablast
Select this option to compare query with closely related sequences and works best if the target percent identity is 95% or more but is very fast.

Also there are advanced options avalailable:

Word Size — Size of subsequence with which search will be conducted.
Gap Costs — Cost to create and extend a gap in an alignment.Increasing the Gap Costs will result in alignments which decrease the number of Gaps introduced.
Match/Mismatch Scores — Reward and penalty for matching and mismatching bases.
Matrix — A key element in evaluating the quality of a pairwise sequence alignment is the "substitution matrix", which assigns a score for aligning any possible pair of residues
Service — Blastp service which needs to be performed: plain, psi or phi.
Filters — Filters for regions of low compositional complexity and repeat elements of the human's genome.
Masks for lookup table only – This option masks only for purposes of constructing the lookup table used by BLAST so that no hits are found based upon low-complexity sequence or repeats (if repeat filter is checked).
Mask Lower Case - With this option selected you can cut and paste a FASTA sequence in upper case characters and denote areas you would like filtered with lower case.

Sometimes database don't respond, therefore you need to re-wait for responce. You can set time that will be spent for re-appeal to database. Note that in case of long sequences time for request preparation increases and search takes several minutes.

Error messages are shown in Log tab.