BLAST against a custom, local database with SequenceServer.
Please cite: Seim et al. (2017) Whole-genome sequence of the metastatic PC3 and LNCaP human prostate cancer cell lines & relevant data sources. Cell-lines authenticated by the QUT Genomics Research Centre.
Could be a temporary network issue, or the service might be configured to "time out" long requests.
Please try again later, or report to the admin or SequenceServer Google Group (if you are the admin) if problem persists.
-evalue <Real> Expectation value (E) threshold for saving hits Default = '10'
-word_size <Integer, >=2> Word size for wordfinder algorithm
-gapopen <Integer> Cost to open a gap
-gapextend <Integer> Cost to extend a gap
-matrix <String> Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0> Minimum word score such that the word is added to the BLAST lookup table
-comp_based_stats <String> Use composition-based statistics for blastp / tblastn: D or d: default (equivalent to 2) 0 or F or f: no composition-based statistics 1: Composition-based statistics as in NAR 29:2994-3005, 2001 2 or T or t : Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties 3: Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally For programs other than tblastn, must either be absent or be D, F or 0 Default = `2'
-num_descriptions <Integer, >=0> Number of database sequences to show one-line descriptions for Default = `500'
-num_alignments <Integer, >=0> Number of database sequences to show alignments for Default = `250'
-seg <String> Filter query sequence with SEG (Format: 'yes', 'window locut hicut', or 'no' to disable) Default = `no'
-soft_masking <Boolean> Apply filtering locations as soft masks Default = `false'
-lcase_masking Use lower case filtering in query and subject sequence(s)?
-gilist <String> Restrict search of database to list of GI's * Incompatible with: negative_gilist, seqidlist, remote, subject, subject_loc
-seqidlist <String> Restrict search of database to list of SeqId's * Incompatible with: gilist, negative_gilist, remote, subject, subject_loc
-negative_gilist <String> Restrict search of database to everything except the listed GIs * Incompatible with: gilist, seqidlist, remote, subject, subject_loc
-entrez_query <String> Restrict search with the given Entrez query * Requires: remote
-db_soft_mask <String> Filtering algorithm ID to apply to the BLAST database as soft masking * Incompatible with: subject, subject_loc
-culling_limit <Integer, >=0> If the query range of a hit is enveloped by that of at least this many higher-scoring hits, delete the hit * Incompatible with: best_hit_overhang, best_hit_score_edge
-best_hit_overhang <Real, (>0 and <0.5)> Best Hit algorithm overhang value (recommended value: 0.1) * Incompatible with: culling_limit
-best_hit_score_edge <Real, (>0 and <0.5)> Best Hit algorithm score edge value (recommended value: 0.1) * Incompatible with: culling_limit
-max_target_seqs <Integer, >=1> Maximum number of aligned sequences to keep
This could take some time depending on the size of your query and database(s).