Clj-biosequence 0.2
Library for the manipulation of biological sequences.
clj-biosequence.blast
Public variables and functions:
- ->blastDB
- ->blastHit
- ->blastHsp
- ->blastIteration
- ->blastParameters
- ->blastReader
- ->blastSearch
- blast
- blast-database
- blast-evalue
- blast-filter
- blast-matrix
- blast-parameter-value
- blast-program
- blast-version
- get-hit-value
- get-hsp-value
- hit-accession
- hit-bit-scores
- hit-def
- hit-e-values
- hit-frames
- hit-seq
- hsp-alignment
- hsp-seq
- init-blast-db
- init-blast-search
- iteration-query-length
- map->blastDB
- map->blastHit
- map->blastHsp
- map->blastIteration
- map->blastParameters
- map->blastReader
- map->blastSearch
- significant-hit-seq
clj-biosequence.core
Public variables and functions:
- ->biosequenceIndex
- ->biosequenceIndexReader
- ->bzipped
- ->fastaFile
- ->fastaReader
- ->fastaSequence
- ->fastaString
- ->gzipped
- ->uncompressed
- ->zipped
- bioReader
- bioreader
- bioseq-proxy
- Biosequence
- biosequence->file
- biosequenceCitation
- biosequenceCitations
- biosequenceComments
- biosequenceDbRef
- biosequenceDbRefs
- biosequenceDescription
- biosequenceEvidence
- biosequenceFeature
- biosequenceFeatures
- biosequenceFile
- biosequenceGene
- biosequenceGenes
- biosequenceGoTerm
- biosequenceGoTerms
- biosequenceID
- biosequenceInterval
- biosequenceIntervals
- biosequenceIO
- biosequenceName
- biosequenceNameObject
- biosequenceNotes
- biosequenceParameters
- biosequenceProtein
- biosequenceProteins
- biosequenceReader
- biosequenceStatus
- biosequenceSubCellLoc
- biosequenceSubCellLocs
- biosequenceSummary
- biosequenceSynonyms
- biosequenceTaxonomies
- biosequenceTaxonomy
- biosequenceTranslation
- biosequenceUrl
- biosequenceVariant
- clean-sequence
- default-biosequence-biosequence
- default-biosequence-citation
- default-biosequence-citations
- default-biosequence-comments
- default-biosequence-dbref
- default-biosequence-dbrefs
- default-biosequence-description
- default-biosequence-evidence
- default-biosequence-feature
- default-biosequence-features
- default-biosequence-file
- default-biosequence-gene
- default-biosequence-genes
- default-biosequence-goterm
- default-biosequence-goterms
- default-biosequence-id
- default-biosequence-interval
- default-biosequence-intervals
- default-biosequence-name
- default-biosequence-nameobject
- default-biosequence-notes
- default-biosequence-protein
- default-biosequence-proteins
- default-biosequence-status
- default-biosequence-subcell
- default-biosequence-subcells
- default-biosequence-summary
- default-biosequence-synonyms
- default-biosequence-tax
- default-biosequence-taxonomies
- default-biosequence-translation
- default-biosequence-url
- default-biosequence-variant
- default-reader
- delete-indexed-biosequence
- fasta-string
- fastaReduce
- get-feature-sequence
- get-interval-sequence
- get-list
- get-one
- get-req
- get-text
- id-convert
- index-biosequence-file
- init-fasta-file
- init-fasta-reader
- init-fasta-sequence
- init-fasta-string
- load-biosequence-index
- make-date
- make-date-format
- map->biosequenceIndex
- map->biosequenceIndexReader
- map->bzipped
- map->fastaFile
- map->fastaReader
- map->fastaSequence
- map->fastaString
- map->gzipped
- map->uncompressed
- map->zipped
- n50
- object->file
- p-key
- parse-date
- post-req
- protein-charge
- return-nil
- reverse-comp
- reverse-seq
- set-bioseq-proxy!
- six-frame-translation
- sub-bioseq
- translate
clj-biosequence.entrezgene
Public variables and functions:
- ->entrezBiosource
- ->entrezDbTag
- ->entrezExtraTerm
- ->entrezGene
- ->entrezGeneComment
- ->entrezGeneConnection
- ->entrezgeneFile
- ->entrezGeneReader
- ->entrezGeneSource
- ->entrezGeneTrack
- ->entrezInterval
- ->entrezMap
- ->entrezOrgName
- ->entrezOrgRef
- ->entrezOtherSource
- ->entrezPcrPrimers
- ->entrezProtein
- ->entrezSeqLocation
- ->entrezSubSource
- default-entrez-comments
- display-string
- entrez-biosource
- entrez-gene-source
- entrez-gene-track
- entrez-location
- entrez-non-unique-keys
- entrez-unique-keys
- entrezComments
- genome
- init-entrezgene-connection
- init-entrezgene-file
- init-gene-reader
- map->entrezBiosource
- map->entrezDbTag
- map->entrezExtraTerm
- map->entrezGene
- map->entrezGeneComment
- map->entrezGeneConnection
- map->entrezgeneFile
- map->entrezGeneReader
- map->entrezGeneSource
- map->entrezGeneTrack
- map->entrezInterval
- map->entrezMap
- map->entrezOrgName
- map->entrezOrgRef
- map->entrezOtherSource
- map->entrezPcrPrimers
- map->entrezProtein
- map->entrezSeqLocation
- map->entrezSubSource
- map-method-type
- map-proxy
- org-name
- org-ref
- origin
- other-sources
- pcr-primers
- pmids
- seq-locations
- source-id
- source-name
- string1
- string2
- subsource
- subsource-attribute
- subsource-name
- subsource-type
- walk-comments
- xtra-terms
clj-biosequence.genbank
Public variables and functions:
- ->genbankCitation
- ->genbankConnection
- ->genbankDbRef
- ->genbankFeature
- ->genbankFile
- ->genbankInterval
- ->genbankQualifier
- ->genbankReader
- ->genbankSequence
- ->genbankString
- ->genbankTaxRef
- feature-location
- filter-qualifiers
- gb-seq-comment
- genbank-search
- get-qualifiers
- init-genbank-connection
- init-genbank-file
- init-genbank-reader
- init-genbank-string
- map->genbankCitation
- map->genbankConnection
- map->genbankDbRef
- map->genbankFeature
- map->genbankFile
- map->genbankInterval
- map->genbankQualifier
- map->genbankReader
- map->genbankSequence
- map->genbankString
- map->genbankTaxRef
- qualifiers
clj-biosequence.uniprot
Public variables and functions:
- ->uniprotCitation
- ->uniprotComment
- ->uniprotConnection
- ->uniprotDbRef
- ->uniprotFeature
- ->uniprotFile
- ->uniprotGene
- ->uniprotInterval
- ->uniprotProtein
- ->uniprotReader
- ->uniprotTaxRef
- init-uniprot-connection
- init-uniprot-file
- map->uniprotCitation
- map->uniprotComment
- map->uniprotConnection
- map->uniprotDbRef
- map->uniprotFeature
- map->uniprotFile
- map->uniprotGene
- map->uniprotInterval
- map->uniprotProtein
- map->uniprotReader
- map->uniprotTaxRef
- uniprot-search