ena_submission

ena_submission list 82 plastif genes
RBGKew · Mar 12, 2022 · fd1bbe4 · fd1bbe4
1 parent 72622cb
commit fd1bbe4
Show file tree

Hide file tree

Showing 11 changed files with 11,436 additions and 2,086 deletions.
diff --git a/ENA_gene_submission.ipynb b/ENA_gene_submission.ipynb
diff --git a/ENA_plastome_submission.ipynb b/ENA_plastome_submission.ipynb
diff --git a/Reference_Genes_from_GB.ipynb b/Reference_Genes_from_GB.ipynb
@@ -3,7 +3,6 @@
   {
    "cell_type": "code",
    "execution_count": 72,
-   "id": "eleven-leadership",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -18,7 +17,6 @@
   {
    "cell_type": "code",
    "execution_count": 73,
-   "id": "composite-machinery",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -47,7 +45,6 @@
   {
    "cell_type": "code",
    "execution_count": 74,
-   "id": "peaceful-colon",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -63,7 +60,6 @@
   {
    "cell_type": "code",
    "execution_count": 75,
-   "id": "terminal-newport",
    "metadata": {},
    "outputs": [
     {
@@ -726,7 +722,6 @@
   {
    "cell_type": "code",
    "execution_count": 76,
-   "id": "racial-impact",
    "metadata": {},
    "outputs": [
     {
@@ -953,7 +948,6 @@
   {
    "cell_type": "code",
    "execution_count": 77,
-   "id": "greek-cisco",
    "metadata": {},
    "outputs": [
     {
@@ -989,7 +983,6 @@
   {
    "cell_type": "code",
    "execution_count": 78,
-   "id": "welsh-longitude",
    "metadata": {},
    "outputs": [
     {
@@ -1028,7 +1021,6 @@
   {
    "cell_type": "code",
    "execution_count": 79,
-   "id": "suited-terrain",
    "metadata": {},
    "outputs": [
     {
@@ -1134,7 +1126,6 @@
   {
    "cell_type": "code",
    "execution_count": 82,
-   "id": "congressional-small",
    "metadata": {},
    "outputs": [
     {
@@ -1625,7 +1616,6 @@
   {
    "cell_type": "code",
    "execution_count": 83,
-   "id": "dated-representation",
    "metadata": {},
    "outputs": [
     {
@@ -1643,7 +1633,6 @@
   {
    "cell_type": "code",
    "execution_count": 84,
-   "id": "detailed-reputation",
    "metadata": {},
    "outputs": [
     {
@@ -1795,7 +1784,6 @@
   {
    "cell_type": "code",
    "execution_count": 86,
-   "id": "czech-comparative",
    "metadata": {},
    "outputs": [
     {
@@ -1912,7 +1900,6 @@
   {
    "cell_type": "code",
    "execution_count": 87,
-   "id": "geographic-perception",
    "metadata": {},
    "outputs": [
     {
@@ -2139,7 +2126,6 @@
   {
    "cell_type": "code",
    "execution_count": 88,
-   "id": "athletic-animation",
    "metadata": {},
    "outputs": [
     {
@@ -2162,7 +2148,6 @@
   {
    "cell_type": "code",
    "execution_count": 96,
-   "id": "arabic-reader",
    "metadata": {},
    "outputs": [
     {
@@ -2188,7 +2173,6 @@
   {
    "cell_type": "code",
    "execution_count": 97,
-   "id": "thousand-binding",
    "metadata": {},
    "outputs": [
     {
@@ -2209,7 +2193,6 @@
   {
    "cell_type": "code",
    "execution_count": 94,
-   "id": "sixth-freedom",
    "metadata": {},
    "outputs": [
     {
@@ -2524,15 +2507,13 @@
   },
   {
    "cell_type": "markdown",
-   "id": "minor-retro",
    "metadata": {},
    "source": [
     "Run 'makeblastdb -in References/cpDNA_RefCDS.fasta -dbtype nucl -parse_seqids'"
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "formal-chile",
    "metadata": {},
    "source": [
     "blastn  -query ../GetOrganelles/PAFTOL/fasta_pt/PAFTOL_016977_pt.fasta  -db References/cpDNA_RefGenes.fasta -outfmt \"6 qseqid sseqid pident length mismatch gapopen qlen qstart qend slen sstart send evalue bitscore qseq\" -out PAFTOL_016977.blast -max_target_seqs 5 -num_threads 1 -gapopen 0 -gapextend 0\n",
@@ -2557,7 +2538,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.8.5"
   }
  },
  "nbformat": 4,