📦 ncbi-tools-bin

36 pages

A

  • asn2all(1)generate reports from ASN.1 biological data✨
  • asn2asn(1)convert NCBI data between text and binary ASN.1✨
  • asn2ff(1)convert ASN.1 biological data to a flat format (old version)✨
  • asn2fsa(1)convert biological sequence data from ASN.1 to FASTA✨
  • asn2gb(1)convert ASN.1 biological data to a GenBank-style flat format✨
  • asn2idx(1)index ASN.1 Bioseq-sets for fast access to individual sequences✨
  • asn2xml(1)translate biological data from ASN.1 to XML✨
  • asndhuff(1)decompress compressed ASN.1 (CASN) files✨
  • asndisc(1)check ASN.1 biological sequence records for discrepancies✨
  • asnmacro(1)process ASN.1 biological data per Sequin macros✨
  • asntool(1)process ASN.1 module specifications✨
  • asnval(1)validate ASN.1 biological sequence records✨

C

  • checksub(1)a validator for NCBI ASN.1 Seq-submit data✨
  • cleanasn(1)clean up irregularities in NCBI ASN.1 objects✨

D

E

  • errhdr(1)produce a C header file from a set of messages✨

F

  • fa2htgs(1)formatter for high throughput genome sequencing project submissions✨
  • findspl(1)find protein splice sites✨

G

  • gbseqget(1)format sequences from GenBank as an XML GBSet✨
  • gene2xml(1)convert NCBI Entrez Gene ASN.1 into XML✨
  • getmesh(1)get MeSH terms from a Medline entry✨
  • getpub(1)look up Medline entries by UID✨
  • gil2bin(1)convert GenInfo integrated IDs to or from binary✨

I

  • idfetch(1)retrieve biological data from the NCBI ID1 server✨
  • indexpub(1)index an ASN.1 Pub-set by Medline UID✨
  • insdseqget(1)format sequences from GenBank as an XML INSDSet✨

M

  • makeset(1)build a Bioseq-set from Seq-entries✨

N

  • nps2gps(1)convert nucleotide-protein sets to ASN.1 genomic product sets✨

S

T

  • taxblast(1)annotate BLAST output with taxonomic details✨
  • tbl2asn(1)prepare a GenBank submission using an ASCII feature table✨
  • trna2sap(1)convert tRNAscan-SE output to an ASN.1 Seq-annot object✨
  • trna2tbl(1)convert tRNAscan-SE output to a Sequin feature table✨

V

  • vecscreen(1)find nucleic acid segments of possible vector origin✨