TDA_Pangenomics

Extracción de datos

Subset - Clavibacter Michiganensis Nebraskensis 1097677.33 link - Clavibacter Michiganensis Nebraskensis 31963.54 link - Clavibacter Michiganensis Nebraskensis 31963.56 link

Rast

Anotar los genomas en rast y descargar los archivos .fasta y .gbk.

Blast

Concatenar archivos y correr BLAST con la opción de prot porque son Pangenomas.

cat ~/blast_Nebraskensis/data/*.faa > all-genomes.faa

mkdir database

makeblastdb -in ~/blast_Nebraskensis/data/all-genomes.faa -dbtype prot -out ~/blast_Nebraskensis/database/all-genomes

Correr blastp con cada uno de los archivos

nohup blastp -query ~/blast_Nebraskensis/data/31963.56.faa -db ~/blast_Nebraskensis/database/all-genomes -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" > ~/blast_Nebraskensis/output-blast/31963.56.blast &

nohup blastp -query ~/blast_Nebraskensis/data/31963.54.faa -db ~/blast_Nebraskensis/database/all-genomes -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" > ~/blast_Nebraskensis/output-blast/31963.54.blast &

nohup blastp -query ~/blast_Nebraskensis/data/1097677.33.faa -db ~/blast_Nebraskensis/database/all-genomes -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore" > ~/blast_Nebraskensis/output-blast/1097677.33.blast &

• qseqid: Query Seq-id
• sseqid: Subject Seq-id
• pident: Percentage of identical matches
• length: Alignment length
• mismatch Number of mismatches
• gapopen: Number of gap openings
• qstart: Start of alignment in query
• qend: End of alignment in query
• sstart: Start of alignment in subject
• send: End if alignment in subject
• evalue: Expect value
• bitscore: Bit score

Concatenar los outputs

cat ~/blast_Nebraskensis/output-blast/*.blast > all-blast.blast

all-blast.blast

all-genomes.blast

all-blast_6genomas.blast

Get_homologues

Correrlo con los algoritmos COG y COML

COG get_homologues.pl -d genomes_gbks -G -t 0 -n 16

COML get_homologues.pl -d genomes_gbks -M -t 0 -c -n 16

Obtenemos familias

for infile in *.faa; do base=$(basename ${infile} .faa); echo -n "${base},"; cat ${infile} | grep '>' | less -S | cut -d' ' -f1 | cut -d'>' -f2 | awk '{print}' ORS=',' | perl -ple 'chop'; done &> families.csv

Obtener pancore_matrix

less -S pancore-matrix.csv | cut -d',' -f1,6 | sort -t ',' -k 2 > ordered-pancore-matrix.csv

Crear matriz de distancias

Scrip para generar la matriz de distancia usando el output de blast.

Script en R

Matriz 3 Genomas

Matriz 6 Genomas

Construir filtración de simplejos

Scrip en Gudhi para crear la filtración de simplejos y analizar su persistencia.

Script en python

Resultados

Se detectan las mismas familias con TDA que con get_homologues y se puede determinar su persistencia y confianza.

Streptomyces

| IDTaxonomy | Genero | Especie | Subespecie | Sepa | Genbankseq | Assemby ID | Rastid | | ----------- | ------------ | -------------- | ---------- | -------------------- | ------------------------------------------------------------- | --------------- | ---------- | | 227882 | Streptomyces | avermitilis | | MA-4680 = NBRC 14893 | BA000030.4 | ASM976v2 | 227882.63 | | 1901 | Streptomyces | clavuligerus | | ATCC 27064 | CM001015.1 | GCA000148465.1 | | | 653045 | Streptomyces | violaceusniger | | Tu 4113 | CP002994.1 | ASM14781v3 | 653045.26 | | 132474 | Streptomyces | rimosus | rimosus | DV3 | CP100443.1 | ASM2422305v1 | 132474.59 | | 100226 | Streptomyces | coelicolor | | A3(2) | AL645882.2 | ASM20383v1 | 100226.232 | | 1343740 | Streptomyces | rapamycinicus | | NRRL 5491 | CP085193.1 | ASM2429896v1 | 1343740.3 | | 1901 | Streptomyces | clavuligerus | | F1D7 | CP065253.1 | ASM1576777v1 | 1901.63 |

All-blast-Streptomyces

Mycoplasma

| IDTaxonomy | Genero | Especie | Subespecie | Sepa | Genbankseq | Assemby ID | | ----------- | -------------- | ---------------------------- | ----------- | ----------- | ----------- | ---------- | | 347257 | Mycoplasmopsis | Mycoplasmopsis agalactiae | | PG2 | CU179680.1 | ASM6360v1 | | 262722 | Mesomycoplasma | Mesomycoplasma hyopneumoniae | | 7448 | AE017244.1 | ASM822v1 | | 272632 | Mycoplasma | Mycoplasma mycoides | mycoides SC | PG1 | BX293980.2 | ASM1144v1 | | 243273 | Mycoplasmoides | Mycoplasmoides genitalium | | G37 | L43967.2 | ASM2732v1 | | 273119 | Ureaplasma | Ureaplasma parvum | serovar 3 | ATCC 700970 | AF222894.1 | ASM662v1 | | 272634 | Mycoplasmoides | Mycoplasmoides pneumoniae | | M129 | U00089.2 | ASM2734v1 | | 1403316 | Mycoplasma | Mycoplasma parvum | | Indiana | CP006771.1 | ASM47741v1 |

All-blast-Mycoplasma

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Equipo

• José María Ibarra Rodríguez
• Adriana Haydeé Contreras Peruyero
• Fernando Altamirano Fernández
• Andrea Chávez Heredia
• Marisol Navarro Miranda
• Cruz Vargas de León