4. Create InterProScan profile

Rbims also includes functions to read and explore InterProScan annotations. To learn how to to this;

First, load the rbims package.

library(rbims)

read_interpro(): Parse InterProScan Outputs

The read_interpro function is designed to parse and format raw output files from the InterProScan annotation tool. Aditionally, this function can parse the information of the KEGG IDs but, the KEGG analysis is just possible if InterProScan was run with the -pa option.

Input Requirements

• File Path: Provide the path to the directory containing your InterProScan files. Even if its just one, the path needs to be explicitly defined for the directory only.

• File Extension: The function specifically looks for files ending in *.tsv.

Data Structure

The processed input contains 15 key columns:

• Protein accession (e.g. P51587)

• Sequence MD5 digest (e.g. 14086411a2cdf1c4cba63020e1622579)

• Sequence length (e.g. 3418)

• Analysis (e.g. Pfam / PRINTS / Gene3D)

• Signature accession (e.g. PF09103 / G3DSA:2.40.50.140)

• Signature description (e.g. BRCA2 repeat profile)

• Start location

• Stop location

• Score - is the e-value (or score) of the match reported by member database method (e.g. 3.1E-52)

• Status - is the status of the match (T: true)

• Date - is the date of the run

• InterPro annotations - accession (e.g. IPR002093)

• InterPro annotations - description (e.g. BRCA2 repeat)

• GO annotations with their source(s), e.g. GO:0005515(InterPro)|GO:0006302(PANTHER)|GO:0007195(InterPro,PANTHER). This is an optional column; only displayed if the –goterms option is switched on

• Pathways annotations, e.g. REACT_71. This is an optional column; only displayed if the –pathways option is switched on

If you want to follow this example, you can download the raw data here.

To obtain a wide output, use the argument profile = T. To explore more databases, the argument database can include the following options:

• “INTERPRO”

• “TIGRFAM”

• “SUPERFAMILY”

• “SMART”

• “SFLD”

• “ProSiteProfiles”

• “ProSitePatterns”

• “ProDom”

• “PRINTS”

• “PIRSF”

• “MobiDBLite”

• “Hamap”

• “Gene3D”

• “Coils”

• “CDD”

interpro_profile_T <-read_interpro(data_interpro = "../test/results/01.iprscan",
                                   database= "Pfam", 
                                   profile = T, 
                                   write = F)

head(interpro_profile_T)

Table 1. InterProScan Profile Overview ( profile = T )

Pfam	domain_name	5mSIPHEX1_0	5mSIPHEX1_1	5mSIPHEX1_10	5mSIPHEX1_11	5mSIPHEX1_13	5mSIPHEX1_15	5mSIPHEX1_18	5mSIPHEX1_19	5mSIPHEX1_2	5mSIPHEX1_25	5mSIPHEX1_26	5mSIPHEX1_32	5mSIPHEX1_33	5mSIPHEX1_37	5mSIPHEX1_8	5mSIPHEX1_9	5mSIPHEX2_10	5mSIPHEX2_14	5mSIPHEX2_16	5mSIPHEX2_18	5mSIPHEX2_25	5mSIPHEX2_3	5mSIPHEX2_5	5mSIPHEX2_7	700mSIPHEX1_0	700mSIPHEX1_1	700mSIPHEX1_12	700mSIPHEX1_15	700mSIPHEX1_17	700mSIPHEX1_18	700mSIPHEX1_2	700mSIPHEX1_20	700mSIPHEX1_3	700mSIPHEX1_8	700mSIPHEX2_13	700mSIPHEX2_14	700mSIPHEX2_16	700mSIPHEX2_21	700mSIPHEX2_22	700mSIPHEX2_23	700mSIPHEX2_24	700mSIPHEX2_9
PF00005	ABC transporter	74	42	76	30	54	21	28	26	27	30	20	28	21	61	100	20	69	78	16	31	91	60	29	54	41	98	36	29	29	36	32	33	76	44	44	29	36	29	33	34	34	83
PF08352	Oligopeptide/dipeptide transporter, C-terminal region	13	4	3	1	7	1	1	0	0	1	0	1	1	6	10	0	12	3	0	1	8	6	0	7	6	11	1	1	1	1	1	1	3	3	3	1	1	1	1	1	2	10
PF06242	Transcriptional cell cycle regulator TrcR	1	1	0	0	1	1	0	0	0	0	0	0	0	1	1	0	1	0	0	0	1	1	0	1	0	1	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	1
PF00586	AIR synthase related protein, N-terminal domain	3	1	2	3	2	4	3	1	3	3	2	4	2	2	2	2	3	2	1	3	2	2	2	2	1	3	3	3	2	3	2	3	2	0	0	2	3	3	2	3	2	3
PF02769	AIR synthase related protein, C-terminal domain	3	1	3	3	2	4	4	1	3	3	2	4	2	2	2	3	3	3	2	3	2	2	2	2	2	3	4	4	3	4	3	3	3	0	0	3	4	4	3	4	3	3
PF02021	Uncharacterised protein family UPF0102	1	1	1	1	1	1	1	1	1	1	0	1	1	1	1	1	1	2	1	1	1	1	1	1	0	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1	1
PF01654	Cytochrome bd terminal oxidase subunit I	1	0	1	1	0	0	0	1	0	1	0	1	1	0	0	2	1	1	0	1	0	0	1	0	1	2	0	1	1	2	3	1	1	0	0	1	2	1	3	0	1	2
PF00528	Binding-protein-dependent transport system inner membrane component	54	30	39	10	31	3	7	8	4	10	0	9	2	40	78	2	53	39	0	10	67	36	9	31	31	59	2	6	2	8	6	12	39	29	29	2	8	6	7	2	18	52
PF00920	Dehydratase family	4	2	3	2	2	2	2	2	2	2	0	2	0	2	5	2	4	3	0	3	4	2	1	2	2	3	1	2	1	2	2	2	3	1	1	1	2	2	2	1	2	3
PF01458	SUF system FeS cluster assembly, SufBD	2	2	2	2	2	2	4	0	2	2	2	2	2	0	2	0	2	2	2	2	2	0	2	2	1	2	2	2	2	0	2	2	2	0	0	2	0	2	2	2	0	2

Or print a long table profile = F.

interpro_profile_T <-read_interpro(data_interpro = "../test/results/01.iprscan",
                                   database= "Pfam", 
                                   profile = T, 
                                   write = F)

head(interpro_profile_F)

Table 1. InterProScan Profile Overview ( profile = F )

Scaffold_name	Bin_name	Pfam	domain_name	Abundance
5mSIPHEX1_0_scaffold_3_c1_201	5mSIPHEX1_0	PF00005	ABC transporter	74
5mSIPHEX1_0_scaffold_3_c1_201	5mSIPHEX1_0	PF08352	Oligopeptide/dipeptide transporter, C-terminal region	13
5mSIPHEX1_0_scaffold_12_c2_232	5mSIPHEX1_0	PF06242	Transcriptional cell cycle regulator TrcR	1
5mSIPHEX1_0_scaffold_9_c1_171	5mSIPHEX1_0	PF00586	AIR synthase related protein, N-terminal domain	3
5mSIPHEX1_0_scaffold_9_c1_171	5mSIPHEX1_0	PF02769	AIR synthase related protein, C-terminal domain	3
5mSIPHEX1_0_scaffold_12_c2_272	5mSIPHEX1_0	PF02021	Uncharacterised protein family UPF0102	1
5mSIPHEX1_0_scaffold_4_c1_367	5mSIPHEX1_0	PF01654	Cytochrome bd terminal oxidase subunit I	1
5mSIPHEX1_0_scaffold_4_c1_39	5mSIPHEX1_0	PF00528	Binding-protein-dependent transport system inner membrane component	54
5mSIPHEX1_0_scaffold_62_c1_152	5mSIPHEX1_0	PF00920	Dehydratase family	4
5mSIPHEX1_0_scaffold_9_c1_116	5mSIPHEX1_0	PF01458	SUF system FeS cluster assembly, SufBD	2

You can export this profile like this:

write.table(interpro_profile_T, "Interpro_profile_T.tsv", 
            quote = F, 
            sep = "\t", 
            row.names = F, 
            col.names = T)

Or setting write write = T in the function read_interpro()