RhesusBase Query System supports three searching types: ID-based Search, Location-based Search and Sequence-based Search.

ID-based Search offers fuzzy searching of Gene Page by ID of different databases or categories. If multiple hits are found, a gene list will be showed for user to choose the interesting gene. If only one hit is found, user will be taken to the corresponding gene page directly.

Location-based Search offers gene location searching of Gene Page in the format of chr:start-end. If location of a gene overlaps with the interesting location, the gene will be picked up as a hit. For multiple hits, a gene list will be showed.

Sequence-based Search offer BLAST search against rhesus macaque RefSeq RNA or protein. The BLAST interface was from SequenceServer which uses NCBI BLAST.

Blast methods

Nucleotide databases

Protein databases


-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'
*** Query filtering options
-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)?
*** Restrict search or results
-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 
						

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