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README.md

Annotations

In this directory we would save the raw outputs of APPRIS per gene.

This directory would contains the following subdirectories:

{APPRIS_version}
        |
        |___ {species_name}
                    |
                    |__ {datasource_version}
                                |
                                |__ {chromosome/gene_id subdirectories}
                                                |
                                                |__ /annotation_files/

APPRIS annotation files

The following files are the raw outputs for a gene generated by APPRIS.

pipeline.ini

Config INI file with the parameters of pipeline.

annot.gtf

Exon features of the gene in GTF format.

Note: Optional output. It is generated when the input of pipeline has exon features.

pannot.gtf

CDS features of the protein in GTF format.

Note: Optional output. It is generated when the input of pipeline has exon features.

transc.fa

Nucleotide sequences of transcripts in FASTA format.

Note: Optional output. It is generated when the input of pipeline has exon features.

transl.fa

Amino-acid sequences of protein-coding transcripts in FASTA format.

cdsseq.fa

Amino-acid sequences of transcripts divided by CDS in FASTA format.

Note: Optional output. It is generated when the input of pipeline has exon features.

firestar

Output of firestar method.

In detail (for each isoform)

  • the peptide position,
  • the functional amino acid,
  • PDB ligand id,
  • Some scores:
    • motif frequency
    • and a score of all predicted catalytic residues. It is a measure of prediction reliablity. The score should be close to six.
    • identity
  • 'C>>' sequence id, consensus residues compared with another isoform
  • 'F>>' sequence id, final no. functional residues
######
13	LMLQQTCPLCKFN	ZN[1.00,6.0,77.8]
16	QQTCPLCKFNVLD	ZN[1.00,6.0,77.8]
>>>ENST00000421022	2	13,16
----------------------------------------------------------------------
F>>	ENST00000421022	2	2

matador3d

Output of Matador3D method.

In detail (for each isoform)

  • '>' sequence id and 3D structure score
  • '-' List of CDS coordinates with the 3D str. score
    • List of fragment of CDS with
      • the protein coord. and align coord.,
      • the 3D str. score,
      • and the best PDB template with the percentage identity of the alignment.
>ENST00000215798	1.28
- 1:32[1]	0
	1:32	-
- 33:80[2]	0
	33:80	-
...
- 274:342[8]	1.08
	274:284[274:284]	0.33[1*1*0.33]	4V3K_F[81.82]
	285:285	-
	286:305[286:305]	0.75[1*1*0.75]	4V3K_F[55.00]
	306:334[306:313]	0[0*1*0.75]	4V3K_F[12.50]
	335:342	-

Note: Optional output. It is generated when the input of pipeline has exon features.

matador3d2

Output of Matador3D2 method (version 2 of Matador3D).

In detail (for each isoform)

  • Gene id
  • Sequence id
  • 3D Structure score (sum of bit-scores)
  • List of the best PDB templates
    • bit-score
    • region alignment
ensembl:ENSG00000099999+refseq:200312	ensembl:ENST00000215798+refseq:+uniprot:H0Y2L4	143	4c9r_A;84.7;0.2;8-145;138	4v3l_C;58.3;6.1;257-305;49

spade

Output of SPADE method.

In detail (for each isoform)

  • '>' sequence id with
    • Sum of bit-score,
    • No. functional domains,
    • No. possibly damaged domains,
    • No. damaged domains,
    • No. wrong domains.
  • Label of type domain
  • PfamScan alignment result (*)
  • '>' sequence id with
    • PfamScan alignment result (*)
      • seq id,
      • alignment start,
      • alignment end,
      • envelope start,
      • envelope end,
      • hmm acc,
      • hmm name,
      • type,
      • hmm start,
      • hmm end,
      • hmm length,
      • bit score,
      • E-value,
      • significance,
      • clan,
      • predicted_active_site_residues
>ENST00000215798	30.1	1	0	0	0
domain	263	303	263	303	PF00097.18	zf-C3HC4	Domain	1	42	42	30.1	2.5e-07	1	CL0229
>ENST00000215798    263    303    263    303 PF00097.18  zf-C3HC4          Domain     1    42    42     30.1   2.5e-07   1 CL0229
#HMM       CriCleeaeepn.llltpCkhkvcssClrkwlksskkvkCplC
#MATCH     C++Cl+ + +++ l ++pCkh+++++C+  wl    +++CplC
#PP        ************999******************..7788****
#SEQ       CAVCLDYFCNKQwLRVLPCKHEFHRDCVDPWLM--LQQTCPLC

corsair

Output of CORSAIR method.

In detail (for each isoform)

  • '>' sequence id with conservation score
  • List of nearest homologue species with
    • the percentage of identity,
    • and the species points
  • List of CDS coordinates with the consv. score for the region
    • List of nearest homologue species for this CDS with
      • the percentage of identity,
      • and the species points
>ENST00000382363	2.7
Homo sapiens	100.00	0.5
Mus musculus	88.13	1.1
Rattus norvegicus	89.45	1.1
	- 30387029:30387313[1:95]	2.7
		Rattus norvegicus	83.16	1.1
		Homo sapiens	100.00	0.5
		Mus musculus	78.95	1.1
...
	- 30379603:30379622[372:377]	2.7
		Rattus norvegicus	83.33	1.1
		Homo sapiens	100.00	0.5
		Mus musculus	83.33	1.1

thump

Output of THUMP method.

In detail (for each isoform)

  • '>' sequence id with the length of sequence
  • Helix start,
  • Helix end,
  • and flag if the helix is damaged.
>ENST00000354749        length 2025 a.a.
helix number 1 start: 534       end: 549
helix number 2 start: 532       end: 542        damaged

crash

Output of CRASH method.

In detail (for each isoform)

  • '>' sequence id with
  • start position of signal
  • end position of signal
  • s_mean
  • d_score
  • c_max
  • s_prob
  • sp_score
  • peptide signal
  • localization
  • reliability
  • tp_score
  • mitochondrial_signal
----------------------------------------------------------------------
id	start	end	s_mean	d_score	c_max	s_prob	sp_score	peptide_signal	localization	reliability	tp_score	mitochondrial_signal
>ENST00000302347	1	23	0.933	0.901	0.999	0.992	4	YES	S	1	-1	NO
>ENST00000320216	1	25	0.056	0.049	0.001	0.000	-4	NO	_	2	-5	NO

proteo

Output of PROTEO method.

In detail (for each isoform)

  • peptide sequence
  • Gene id
  • Isoform id
  • No. experiments found
AGPGSLELCGLPSQK,ENSG00000160208.12,ENST00000340648.5,,7
APAMQPAEIQFAQR,ENSG00000160208.12,ENST00000340648.5,,6

Note: Optional output. It is generated when we have already annotations from proteomic data. For the moment, only for the human gene set of GENCODE/Ensembl.

appris

Output of APPRIS with the scores for all methods and the final annotation.

In detail (for each isoform)

  • Gene id
  • Gene name
  • Transcript id
  • Protein id
  • TRANSLATION/NO_TRANSLATION tag
  • Biotype of transcript
  • Start/stop codons found
  • CCDS id
  • TSL type
  • No. functional residues
  • 3D structure score
  • Conservation score
  • Domains score
  • No. transmembrane helices
  • Scores of peptide signal and mitochondrial_signal
  • '-' (INERTIA score - DEPRECATED)
  • No. mapping peptides
  • Principal isoform score
  • Principal isoform label
ENSG00000160255	ITGB2	ENST00000355153	ENSP00000347279	TRANSLATION	protein_coding	-	CCDS13716	2	769	15	14.84	2.6	557.6	1	4,-1	-	36	18	PRINCIPAL:1
ENSG00000160255	ITGB2	ENST00000397854	ENSP00000380952	TRANSLATION	protein_coding	-	-	1	712	9	13.18	0	484.8	1	4,-1	-	32	14.142	MINOR
ENSG00000160255	ITGB2	ENST00000522688	ENSP00000428125	TRANSLATION	protein_coding	stop	-	4	49	0	1.33	0	0	0	-4,-5	-	1	-1	MINOR

appris.label

Output of APPRIS with the labels for all methods and the final annotation.

In detail (for each isoform)

  • Gene id
  • Gene name
  • Transcript id
  • Protein id
  • TRANSLATION/NO_TRANSLATION tag
  • Biotype of transcript
  • Start/stop codons found
  • CCDS id
  • TSL type
  • firestar label
  • Matador3D (or Matador3D2) label
  • CORSAIR label
  • SPADE label
  • THUMP label
  • CRASH label
  • '-' (INERTIA label - DEPRECATED)
  • '-' (PROTEO label - NOT USED)
  • APPRIS label
  • Principal isoform label
ENSG00000160255	ITGB2	ENST00000355153	ENSP00000347279	TRANSLATION	protein_coding	-	CCDS13716	2	769	UNKNOWN	UNKNOWN	UNKNOWN	UNKNOWN	UNKNOWN	YES,NO	-	-	YES	PRINCIPAL:1
ENSG00000160255	ITGB2	ENST00000397854	ENSP00000380952	TRANSLATION	protein_coding	-	-	1	712	NO	NO	NO	NO	UNKNOWN	YES,NO	-	-	NO	MINOR
ENSG00000160255	ITGB2	ENST00000522688	ENSP00000428125	TRANSLATION	protein_coding	stop	-	4	49	NO	NO	NO	NO	NO	NO,NO	-	-	NO	MINOR

appris.nscore

Output of APPRIS with the normalized scores for all methods and the final annotation.

log

Log file.

Note: Optional output.