Other GeneFinder Controls

GeneFinder predictions can be saved as Sequence objects by chosing [Fix temp_gene] from the GeneFind.. menu. Genes can be removed by picking a gene on the fmap and selecting [Remove Gene]. Both of these operations require write access to the database.

Gene predictions can be dumped into an EMBL feature table by selecting the [EMBL dump] option from the menu which is activated by picking the white fmap background. The option [Import Sequence] from the same menu allows a sequence file (in plain or FASTA format) to be read into the fmap. Both these operations do not require write access.

An example of an EMBL dump is given below. Note that the /organism identifier is C. elegans by default.

XX
FH   Key             Location/Qualifiers
FH
FT   source          1..7079
FT                   /organism="Caenorhabditis elegans"
FT                   /clone="EM:X56564"
FT   CDS             join(911..925,961..986,
FT                   1027..1099,1139..1214,1260..1319,
FT                   1412..1518,1566..6467)
FT                   /gene="rpb1"
FT   CDS             join(911..925,961..986,
FT                   1027..1099,1139..1214,1260..1319,
FT                   1412..1518,1566..6467)
FT                   /product="temp_gene"
XX
SQ   Sequence  7079 BP;   2024 A; 1386 C; 1394 G; 2275 T; 0 other;
     aagcttctag agccactcct gacattaaag aacagcatgc taagaaaccg aagcgaaagc
     acacccgttc aacagtacct acaagcaatg ttgaaccagt ttctcaacct caaccctctc
     ctgacaaaat cgtttctagc cccaatccgc catcagcgaa aagggaaaaa aagaaacgtc
     gcaaaagctc gatgtcttct tccattacca ......etc.

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