This is a test version of Biostars. For the public version, visit https://www.biostars.org.
sequence gi number of updated sequences

Hello,

I have a question regarding sequence gi number.

If I have 2 versions of blast database say OldDatabaseVersion and NewDatabaseVersion. The NewDatabaseVersion may have new sequences added, some sequences removed, or some sequences modified.

If the sequence is removed from OldDatabaseVersio, Is its gi number will be used for another sequence? If the sequence is modified, Is its gi number in the OldDatabaseVersion will be the same as its gi number in the NewDatabaseVersion or another gi number will be assigned to it in the NewDatabaseVersion?

Thanks.

gi blast ncbi sequence
• 2,468 views • link
updated by piet piet • written by arfaj a • arfaj a

1 answer

GI numbers are the primary keys in NCBI nucleotide database. Entries in this database may become obsolete or invisible (after request of the submitter), but entries are never removed. Thus is is safe to use GI numbers to compare two versions of your Blast database.

• 0 views • link
written by piet piet

Blast output to any query gives out first few letters in the Fasta header of both query and hits whether it has gi or new accession.version format it will be present in output.

• 0 views • link
written by Naren Naren

Log in to answer this question.

More posts like this
  • GI numbers in NCBI
    written by Christoph • Christoph
    In 2016 NCBI announced that it will phase out GI numbers. https://ncbiinsights.ncbi.nlm.nih.gov/2016/09/12/the-future-of-existing-gi-numbers-at-ncbi/ And the documentation says: "Special note for sequence databases. NCBI is no longer …
  • RNASeq alignment and quantification for a transgenic mouse
    written by viktorfeketa • viktorfeketa
    I have RNASeq data coming from a transgenic mouse (where a single gene's coding sequence is replaced by the gene sequence from another organism). I …
  • Separating mixed bacterial 16S RNA sequences from eukaryotic 18S ITS sequences?
    written by Lionel12 • Lionel12
    A bit of back ground - I have been given thousands of reads in FASTQ format containing sequences (16S and 18S ITS) sequenced by ILLUMINA. …
  • single line fasta to mult line fasta
    written by User 6777 • User 6777
    I know for the reverse procedure, there are lots of methods available. But how can I change my fasta file with sequences like: >gi|189094002 MDDAELNAIRQARLAELQRNAAGGGSSTNPSSSSSGGAQDSAQENMTITILNRVLTNEARERLSRQQTKITFNRKNIAADDDEDDDDFFD …
  • run fadiff to compare fasta files
    written by arfaj a • arfaj a
    Hello, I want to extract the differences from two versions of one blast database. I am using php to do this task. first, i extract …
  • Download nucleotide sequences database
    written by arfaj a • arfaj a
    <p>Hello,</p> <p>I want to build a BLAST tool to compare DNA seq with DNA database ex: GenBank.</p> <p>And I want to store the DNA sequences …
  • gDNA annotation, exon and intron boundary identification
    written by chethusomashekar • chethusomashekar
    Dear Biostars members, Hi, I am Chethana from India, working on multigene phylogenetic analysis of Colletotrichum species prevalent in India on varied host. I am …
  • Modifying fasta header
    written by empyrean999 empyrean999
    I have strange fasta headers like this for some good number of sequences, >gi|61221638|sp|P0A366.1| >gi|61221640|sp|P0A368.1|CR1AA_BACTE RecName: Full= protein synthase>gi|40267|emb|CAA31886.1| unnamed protein product HTSIDGRPINQGNFSATMSSGSNLQSGSFRTVGFTTPFNFSNGSSVFTLSAHVFNSGNEVYIDRIEFVPAEVTFEAEYDLERAQKAVNELFTSSNQIGLKTDVTDYHIDQVSNLVECLSDEFCLDEKQELSEKVKHAKRLSDERNLLQDPNFRGINRQLDRGWRGSTDITIQGGDDVFKENYVTLLGTFDECYPTYLYQKIDESKLKAYTRYQLRGYIEDSQDLEIYLIRYNAKHETVNVPGTGSLWPLSAQSPIGKCGEPNRCAPHLEWNPDLDCSCRDGEKCAHHSHHFSLDIDVGCTDLNEDLGVWVIFKIKTQDGHARLGNLEFLEEKPLVGEALARVKRAEKKWRDKREKLEWETNIVYKEAKESVDALFVNSQYDQLQADTNIAMIHAADKRVHSI I would …
  • Strategizing Blast Result Parsing
    written by Zach Powers Zach Powers
    <p>I have a set of ~200 known sequences of a particular domain that I want to use to fish out similar sequences from NCBI-NT.As you …
  • Get Pairwise Sequence Identity
    written by Chris • Chris
    <p>Hey,</p> <p>for some project I need to run pairwise sequence alignments (local ones, i.e. Smith-Waterman) on protein sequences in order to produce a similarity matrix …